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add nextflow d30e48d

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Kevin
2026-04-29 23:01:54 +02:00
parent d0b12d668d
commit 97cc9058d3
2840 changed files with 730250 additions and 0 deletions
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14
nextflow/tests-v1/checks/.PARSER-V1 Normal file
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# ADDITIONAL TESTS TO VERIFY THE V1 PARSER
complex-names.nf
env-out.nf
env2.nf
error-finish.nf
output-globs.nf
output-dsl.nf
output-val.nf
publish-saveas.nf
singleton.nf
subworkflow.nf
task-retry.nf
tuples.nf
when-block.nf

17
nextflow/tests-v1/checks/ampa.nf/.checks Normal file
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#
# run normal mode
#
$NXF_RUN $WITH_DOCKER --out result.txt | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 5 ]] || false
cmp .expected <(sort .stdout) || false
#
# run resume mode
#
$NXF_RUN $WITH_DOCKER --out result.txt -resume | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 5 ]] || false
cmp .expected <(sort .stdout) || false

15
nextflow/tests-v1/checks/ampa.nf/.expected Normal file
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# This protein has 0 bactericidal stretches
# This protein has 0 bactericidal stretches
# This protein has 0 bactericidal stretches
# This protein has 0 bactericidal stretches
# This protein has 0 bactericidal stretches
# This protein has a mean antimicrobial value of 0.235
# This protein has a mean antimicrobial value of 0.25
# This protein has a mean antimicrobial value of 0.251
# This protein has a mean antimicrobial value of 0.266
# This protein has a mean antimicrobial value of 0.28

19
nextflow/tests-v1/checks/basic.nf/.checks Normal file
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set -e
#
# run normal mode
#
$NXF_RUN | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 2 ]] || false
diff .expected .stdout || false
#
# run resume mode
#
$NXF_RUN -resume | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 2 ]] || false
diff .expected .stdout || false

15
nextflow/tests-v1/checks/basic.nf/.expected Normal file
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Aoba1>
SPVWGQGNKTQAECWEGNHNYGLVRLKEGKTISLTNDGSAVFDYLAVFLN
NVPTIYN
Bscy1>
YGEKDNLRAWWWEIEDEDERHIITMCDGEKMPLEDDNQPEYDWLAYIVGK
PYLGLLNRPV
thp1>
GIEEPRAEQGDSFGLAVLSGKNVTLIDGLHLDIDEEREKKYDYLARYQYG
PSIKKRGIYEVYTGPFDGREGTTENYGNLW
eiv1>
IRELAAVPYIQVSGPHAESEVAYGEPTLNTCYWGVIQGQWAAGSKKRVRD
N
Avhi1>
DRIIKAKRRPVVKIDSNDQIVVAGEGKWLLKAPGKWVPDRSDRYYVRFN

19
nextflow/tests-v1/checks/blast-parallel.nf/.checks Normal file
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set -e
#
# run normal mode
#
$NXF_RUN $WITH_DOCKER > stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > blast'` == 5 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > extract'` == 5 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > align'` == 1 ]] || false
#
# run resume mode
#
$NXF_RUN $WITH_DOCKER -resume > stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process > blast'` == 5 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > extract'` == 5 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > align'` == 1 ]] || false

284
nextflow/tests-v1/checks/blast-parallel.nf/.expected Normal file
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CLUSTAL FORMAT for T-COFFEE Version_11.00.8cbe486 [http://www.tcoffee.org] [MODE: ], CPU=0.00 sec, SCORE=338, Nseq=18, Len=694
lcl|1VIE_A VF-------PS----NA---------------------------T-----
lcl|1IHU_A MQFL-----QNIPPY-LFFTGKGGVGKTSISCATAIRLAEQGKRVLLVST
lcl|1ABO_B MND------PN-----L---------------------------------
lcl|1ABO_A MND------PN-----L---------------------------------
lcl|1YCS_B PEITGQVSLPP---GKR---------------------------TNL---
lcl|1IHD_C LPN-------------I---------------------------------
lcl|1IHW_B MIQ-----------------------------------------------
lcl|1IHW_A MIQ-----------------------------------------------
lcl|1IHV_B MIQ-----------------------------------------------
lcl|1IHV_A MIQ-----------------------------------------------
lcl|1YCS_A SS-----SVPS----QK---------------------------T-----
lcl|1PHT_A MS------------------------------------------------
lcl|1YCS_B_1 PEITGQVSLPP---GKR---------------------------TNL---
lcl|1YCS_B_2 PEITGQVSLPP---GKR---------------------------TNL---
lcl|1YCS_B_3 PEITGQVSLPP---GKR---------------------------TNL---
lcl|1ABO_B_1 MND------PN-----L---------------------------------
lcl|1ABO_A_1 MND------PN-----L---------------------------------
lcl|1PHT_A_1 MS------------------------------------------------
lcl|1VIE_A -----------F------------------------GM-GDRVR------
lcl|1IHU_A DPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRARIVDPIK
lcl|1ABO_B ----------------------------------------FVA-------
lcl|1ABO_A ----------------------------------------FVA-------
lcl|1YCS_B ------RKTGSER-----------------------IAHGMRVKF-----
lcl|1IHD_C ------------------------------------------------T-
lcl|1IHW_B ---------------------------------------NFRVYY-----
lcl|1IHW_A ---------------------------------------NFRVYY-----
lcl|1IHV_B ---------------------------------------NFRVYY-----
lcl|1IHV_A ---------------------------------------NFRVYY-----
lcl|1YCS_A -----------YQ-----------------------GSYGFRLGF-----
lcl|1PHT_A --------------------------------------------------
lcl|1YCS_B_1 ------RKTGSER-----------------------IAHGMRVKF-----
lcl|1YCS_B_2 ------RKTGSER-----------------------IAHGMRVKF-----
lcl|1YCS_B_3 ------RKTGSER-----------------------IAHGMRVKF-----
lcl|1ABO_B_1 ----------------------------------------FVA-------
lcl|1ABO_A_1 ----------------------------------------FVA-------
lcl|1PHT_A_1 --------------------------------------------------
lcl|1VIE_A --------------------------KKSGA-------------------
lcl|1IHU_A GVLPDDVVSSINEQLSGACTTEIAAFDE-FTGLLTDASLLTRFDHIIFDT
lcl|1ABO_B --------------------------------------------------
lcl|1ABO_A --------------------------------------------------
lcl|1YCS_B --------------------------NPLPLALLLDSSLEGEFDLV----
lcl|1IHD_C -------------------------------ILATGGTIAGGGDSA----
lcl|1IHW_B --------------------------------------------------
lcl|1IHW_A --------------------------------------------------
lcl|1IHV_B --------------------------------------------------
lcl|1IHV_A --------------------------------------------------
lcl|1YCS_A --------------------------LHSGTA------------------
lcl|1PHT_A --------------------------------------------------
lcl|1YCS_B_1 --------------------------NPLPLALLLDSSLEGEFDLV----
lcl|1YCS_B_2 --------------------------NPLPLALLLDSSLEGEFDLV----
lcl|1YCS_B_3 --------------------------NPLPLALLLDSSLEGEFDLV----
lcl|1ABO_B_1 --------------------------------------------------
lcl|1ABO_A_1 --------------------------------------------------
lcl|1PHT_A_1 --------------------------------------------------
lcl|1VIE_A --------------------------------------------------
lcl|1IHU_A APTGHTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEAL
lcl|1ABO_B --------------------------------------------------
lcl|1ABO_A --------------------------------------------------
lcl|1YCS_B --------------------------------------------------
lcl|1IHD_C --------------------------------------------------
lcl|1IHW_B --------------------------------------------------
lcl|1IHW_A --------------------------------------------------
lcl|1IHV_B --------------------------------------------------
lcl|1IHV_A --------------------------------------------------
lcl|1YCS_A --------------------------------------------------
lcl|1PHT_A --------------------------------------------------
lcl|1YCS_B_1 --------------------------------------------------
lcl|1YCS_B_2 --------------------------------------------------
lcl|1YCS_B_3 --------------------------------------------------
lcl|1ABO_B_1 --------------------------------------------------
lcl|1ABO_A_1 --------------------------------------------------
lcl|1PHT_A_1 --------------------------------------------------
lcl|1VIE_A --------------------------------------------------
lcl|1IHU_A SDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEA
lcl|1ABO_B --------------------------------------------------
lcl|1ABO_A --------------------------------------------------
lcl|1YCS_B --------------------------------------------------
lcl|1IHD_C --------------------------------------------------
lcl|1IHW_B --------------------------------------------------
lcl|1IHW_A --------------------------------------------------
lcl|1IHV_B --------------------------------------------------
lcl|1IHV_A --------------------------------------------------
lcl|1YCS_A --------------------------------------------------
lcl|1PHT_A --------------------------------------------------
lcl|1YCS_B_1 --------------------------------------------------
lcl|1YCS_B_2 --------------------------------------------------
lcl|1YCS_B_3 --------------------------------------------------
lcl|1ABO_B_1 --------------------------------------------------
lcl|1ABO_A_1 --------------------------------------------------
lcl|1PHT_A_1 --------------------------------------------------
lcl|1VIE_A --------------------------------------------------
lcl|1IHU_A ANDTLAAAI----------WEREQEALANLPADLAGLPTDTLFLQPVNMV
lcl|1ABO_B --------------------------------------------------
lcl|1ABO_A --------------------------------------------------
lcl|1YCS_B -----QRIIYEVDDPSLPND-----------------------------E
lcl|1IHD_C -----TKSN----------YTVG-------------------------KV
lcl|1IHW_B --------------------------------------------------
lcl|1IHW_A --------------------------------------------------
lcl|1IHV_B --------------------------------------------------
lcl|1IHV_A --------------------------------------------------
lcl|1YCS_A --------------------------------------------------
lcl|1PHT_A -------------A------------------------------------
lcl|1YCS_B_1 -----QRIIYEVDDPSLPND-----------------------------E
lcl|1YCS_B_2 -----QRIIYEVDDPSLPND-----------------------------E
lcl|1YCS_B_3 -----QRIIYEVDDPSLPND-----------------------------E
lcl|1ABO_B_1 --------------------------------------------------
lcl|1ABO_A_1 --------------------------------------------------
lcl|1PHT_A_1 -------------A------------------------------------
lcl|1VIE_A --------------------------------------------------
lcl|1IHU_A GVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLI---
lcl|1ABO_B --------------------------------------------------
lcl|1ABO_A --------------------------------------------------
lcl|1YCS_B GITALHN------------------------------AVCAGHTEIVKFL
lcl|1IHD_C GVE-----------------------------------------------
lcl|1IHW_B --------------------------------------------------
lcl|1IHW_A --------------------------------------------------
lcl|1IHV_B --------------------------------------------------
lcl|1IHV_A --------------------------------------------------
lcl|1YCS_A -----KS------------------------------VTC----------
lcl|1PHT_A --------------------------------------------------
lcl|1YCS_B_1 GITALHN------------------------------AVCAGHTEIVKFL
lcl|1YCS_B_2 GITALHN------------------------------AVCAGHTEIVKFL
lcl|1YCS_B_3 GITALHN------------------------------AVCAGHTEIVKFL
lcl|1ABO_B_1 --------------------------------------------------
lcl|1ABO_A_1 --------------------------------------------------
lcl|1PHT_A_1 --------------------------------------------------
lcl|1VIE_A -------------AWQGQIVGWYCTNLTPE--GYAVES----EAHPGSVQ
lcl|1IHU_A ----------------------------------M---------------
lcl|1ABO_B --------------------------------------------------
lcl|1ABO_A --------------------------------------------------
lcl|1YCS_B VQFGVNVNAADSDGWTPLHCAASCNNVQVC--KFLVES----GAAVFAMT
lcl|1IHD_C ----------------------------------N---------------
lcl|1IHW_B -------R------------------------------------------
lcl|1IHW_A -------R------------------------------------------
lcl|1IHV_B -------R------------------------------------------
lcl|1IHV_A -------R------------------------------------------
lcl|1YCS_A -------------TYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMA
lcl|1PHT_A --------------------------------------------------
lcl|1YCS_B_1 VQFGVNVNAADSDGWTPLHCAASCNNVQVC--KFLVES----GAAVFAMT
lcl|1YCS_B_2 VQFGVNVNAADSDGWTPLHCAASCNNVQVC--KFLVES----GAAVFAMT
lcl|1YCS_B_3 VQFGVNVNAADSDGWTPLHCAASCNNVQVC--KFLVES----GAAVFAMT
lcl|1ABO_B_1 --------------------------------------------------
lcl|1ABO_A_1 --------------------------------------------------
lcl|1PHT_A_1 --------------------------------------------------
lcl|1VIE_A -----I--------------------------------------------
lcl|1IHU_A -------------------------------------------LMGKGGV
lcl|1ABO_B -------------------------------------------LYDFVAS
lcl|1ABO_A -------------------------------------------LYDFVAS
lcl|1YCS_B YSDMQTAADKCEEMEEGYTQCSQFLYGVQEKMGIMNKGV-IYALWDYEPQ
lcl|1IHD_C -------------------------------------------LVNAVPQ
lcl|1IHW_B ------------------------------------------DSRDPVWK
lcl|1IHW_A ------------------------------------------DSRDPVWK
lcl|1IHV_B ------------------------------------------DSRDPVWK
lcl|1IHV_A ------------------------------------------DSRDPVWK
lcl|1YCS_A -----I--------------------------------------------
lcl|1PHT_A ------------------------------------EGYQYRALYDYKKE
lcl|1YCS_B_1 YSDMQTAADKCEEMEEGYTQCSQFLYGVQEKMGIMNKGV-IYALWDYEPQ
lcl|1YCS_B_2 YSDMQTAADKCEEMEEGYTQCSQFLYG-----------------------
lcl|1YCS_B_3 YSDMQTAADKCEEMEEGYTQCSQFLYGVQEKMGIMNKGV-IYALWDYEPQ
lcl|1ABO_B_1 -------------------------------------------LYDFVAS
lcl|1ABO_A_1 -------------------------------------------LYDFVAS
lcl|1PHT_A_1 ------------------------------------EGYQYRALYDYKKE
lcl|1VIE_A --------------------------------------------------
lcl|1IHU_A GKTTMAAAIAVRLADMGFD------VHLTTSDP-------AAHLS-MTLN
lcl|1ABO_B GDNTLS----ITKGEKLRV--------LGYNH-------NGEWCE---AQ
lcl|1ABO_A GDNTLS----ITKGEKLRV--------LGYNH-------NGEWCE---AQ
lcl|1YCS_B NDDELPM----KEGDCMTI--------IHREDED-----EIEWWW---AR
lcl|1IHD_C -LKDIA----NVKGEQVVN--------IGSQDMN-----DNVWLT---LA
lcl|1IHW_B GPAKL-----LWKGEGAVV--------IQDNS-------DIK--------
lcl|1IHW_A GPAKL-----LWKGEGAVV--------IQDNS-------DIK--------
lcl|1IHV_B GPAKL-----LWKGEGAVV--------IQDNS-------DIK--------
lcl|1IHV_A GPAKL-----LWKGEGAVV--------IQDNS-------DIK--------
lcl|1YCS_A --------------------------------------------------
lcl|1PHT_A REEDIDL----HLGDILTVNKGSLVA-LGFSDGQEARPEEIGWLNGY-NE
lcl|1YCS_B_1 NDDELPM----KEGDCMTI--------IHREDED-----EIEWWW---AR
lcl|1YCS_B_2 --------------------------------------------------
lcl|1YCS_B_3 NDDELPM----KEGDCMTI--------IHREDED-----EIEWWW---AR
lcl|1ABO_B_1 GDNTLS----ITKGEKLRV--------LGYNH-------NGEWCE---AQ
lcl|1ABO_A_1 GDNTLS----ITKGEKLRV--------LGYNH-------NGEWCE---AQ
lcl|1PHT_A_1 REEDIDL----HLGDILTVNKGSLVA-LGFSDGQEARPEEIGWLNGY-NE
lcl|1VIE_A --------------------------------------------------
lcl|1IHU_A GSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTE
lcl|1ABO_B --TK----------------------------------------------
lcl|1ABO_A --TK----------------------------------------------
lcl|1YCS_B -L-N----------------------------------------------
lcl|1IHD_C KKIN----------------------------------------------
lcl|1IHW_B --------------------------------------------------
lcl|1IHW_A --------------------------------------------------
lcl|1IHV_B --------------------------------------------------
lcl|1IHV_A --------------------------------------------------
lcl|1YCS_A --------------------------------------------------
lcl|1PHT_A -T-T----------------------------------------------
lcl|1YCS_B_1 -L-N----------------------------------------------
lcl|1YCS_B_2 --------------------------------------------------
lcl|1YCS_B_3 -L-N----------------------------------------------
lcl|1ABO_B_1 --TK----------------------------------------------
lcl|1ABO_A_1 --TK----------------------------------------------
lcl|1PHT_A_1 -T-T----------------------------------------------
lcl|1VIE_A --------------------------------------------------
lcl|1IHU_A EIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGE
lcl|1ABO_B --------------------------------------------------
lcl|1ABO_A --------------------------------------------------
lcl|1YCS_B --------------------------------------------------
lcl|1IHD_C -------------TDCDKT-------------------------------
lcl|1IHW_B --------------------------------------------------
lcl|1IHW_A --------------------------------------------------
lcl|1IHV_B --------------------------------------------------
lcl|1IHV_A --------------------------------------------------
lcl|1YCS_A --------------------------------------------------
lcl|1PHT_A --------------------------------------------------
lcl|1YCS_B_1 --------------------------------------------------
lcl|1YCS_B_2 --------------------------------------------------
lcl|1YCS_B_3 --------------------------------------------------
lcl|1ABO_B_1 --------------------------------------------------
lcl|1ABO_A_1 --------------------------------------------------
lcl|1PHT_A_1 --------------------------------------------------
lcl|1VIE_A --------------------------------------------------
lcl|1IHU_A KGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGW
lcl|1ABO_B ---------------------------------------------NGQGW
lcl|1ABO_A ---------------------------------------------NGQGW
lcl|1YCS_B ---------------------------------------------DKEGY
lcl|1IHD_C --------------------------------------------------
lcl|1IHW_B -------------------------------------------------V
lcl|1IHW_A -------------------------------------------------V
lcl|1IHV_B -------------------------------------------------V
lcl|1IHV_A -------------------------------------------------V
lcl|1YCS_A --------------------------------------------------
lcl|1PHT_A ---------------------------------------------GERGD
lcl|1YCS_B_1 ---------------------------------------------DKEGY
lcl|1YCS_B_2 --------------------------------------------------
lcl|1YCS_B_3 ---------------------------------------------DKEGY
lcl|1ABO_B_1 ---------------------------------------------NGQGW
lcl|1ABO_A_1 ---------------------------------------------NGQGW
lcl|1PHT_A_1 ---------------------------------------------GERGD
lcl|1VIE_A Y-PVAA-LERI---------------------N-----------
lcl|1IHU_A I-INNS-LSIADTRSPLLRMRAQQELPQIESVKR----QHAS--
lcl|1ABO_B V-PSNY-ITPV---------------------NS----------
lcl|1ABO_A V-PSNY-ITPV---------------------NS----------
lcl|1YCS_B V-PRNL-LGLY---------------------PRIKPRQRSL-A
lcl|1IHD_C --------------------------------------------
lcl|1IHW_B V-PRRKA-KII----------------------RD---------
lcl|1IHW_A V-PRRKA-KII----------------------RD---------
lcl|1IHV_B V-PRRKA-KII----------------------RD---------
lcl|1IHV_A V-PRRKA-KII----------------------RD---------
lcl|1YCS_A YKQSQHMTEV----------------------V-----------
lcl|1PHT_A F-PGTY-VEYI---------------------GR----KKISPP
lcl|1YCS_B_1 V-PRNL-LGLY---------------------PRIKPRQRSL-A
lcl|1YCS_B_2 --------------------------------------------
lcl|1YCS_B_3 V-PRNL-LGLY---------------------PRIKPRQRSL-A
lcl|1ABO_B_1 V-PSNY-ITPV---------------------NS----------
lcl|1ABO_A_1 V-PSNY-ITPV---------------------NS----------
lcl|1PHT_A_1 F-PGTY-VEYI---------------------GR---------K

20
nextflow/tests-v1/checks/blast.nf/.checks Normal file
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set -e
#
# run normal mode
#
$NXF_RUN $WITH_DOCKER | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > blast'` == 5 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > sort'` == 1 ]] || false
diff .expected .stdout || false
#
# run resume mode
#
$NXF_RUN $WITH_DOCKER -resume | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process > blast'` == 5 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > sort'` == 1 ]] || false
diff .expected .stdout || false

34
nextflow/tests-v1/checks/blast.nf/.expected Normal file
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@@ -0,0 +1,34 @@
1aboA 1ABO:A 100.00 57 0 0 1 57 5 61 2e-40 120
1aboA 1ABO:B 100.00 57 0 0 1 57 5 61 2e-40 120
1aboA 1IHD:A 36.11 36 21 1 5 40 287 320 0.62 18.1
1aboA 1IHD:A 75.00 8 2 0 28 35 179 186 0.69 17.7
1aboA 1IHD:C 36.11 36 21 1 5 40 287 320 0.62 18.1
1aboA 1IHD:C 75.00 8 2 0 28 35 179 186 0.69 17.7
1aboA 1YCS:B 25.49 51 36 1 5 53 175 225 3e-04 27.3
1ihvA 1IHN:A 35.00 20 13 0 25 44 72 91 7.0 14.6
1ihvA 1IHN:A 66.67 9 3 0 35 43 28 36 3.7 15.4
1ihvA 1IHN:B 35.00 20 13 0 25 44 72 91 7.0 14.6
1ihvA 1IHN:B 66.67 9 3 0 35 43 28 36 3.7 15.4
1ihvA 1IHU:A 27.27 33 24 0 8 40 534 566 5.5 15.0
1ihvA 1IHV:A 100.00 49 0 0 1 49 4 52 3e-32 99.8
1ihvA 1IHV:B 100.00 49 0 0 1 49 4 52 3e-32 99.8
1ihvA 1IHW:A 100.00 49 0 0 1 49 4 52 3e-32 99.8
1ihvA 1IHW:B 100.00 49 0 0 1 49 4 52 3e-32 99.8
1ihvA 1YCS:A 54.55 11 5 0 1 11 107 117 0.88 17.3
1pht 1IHF:B 33.33 21 14 0 53 73 60 80 0.75 18.1
1pht 1IHS:H 32.00 25 17 0 40 64 175 199 4.0 16.5
1pht 1IHT:H 32.00 25 17 0 40 64 175 199 4.0 16.5
1pht 1PHT:A 100.00 80 0 0 1 80 5 84 1e-56 164
1pht 1YCS:B 23.08 26 20 0 19 44 115 140 3.4 16.5
1pht 1YCS:B 30.43 23 16 0 6 28 175 197 0.015 23.5
1vie 1IHM:A 31.82 22 11 1 19 40 343 360 9.0 14.6
1vie 1IHM:B 31.82 22 11 1 19 40 343 360 9.0 14.6
1vie 1IHM:C 31.82 22 11 1 19 40 343 360 9.0 14.6
1vie 1IHU:A 26.92 26 18 1 25 49 156 181 8.5 14.6
1vie 1VIE:A 100.00 51 0 0 1 51 12 62 1e-35 108
1ycsB 1ABO:A 24.07 54 39 1 3 56 6 57 4e-05 28.5
1ycsB 1ABO:B 24.07 54 39 1 3 56 6 57 4e-05 28.5
1ycsB 1IHU:A 35.71 14 9 0 6 19 251 264 6.9 15.4
1ycsB 1PHT:A 30.43 23 16 0 6 28 10 32 0.013 22.3
1ycsB 1YCS:B 100.00 60 0 0 1 60 170 229 3e-42 131

21
nextflow/tests-v1/checks/buffer.nf/.checks Normal file
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@@ -0,0 +1,21 @@
set -e
#
# run normal mode
#
$NXF_RUN | tee .stdout
[[ `grep -c 'Submitted process > blastThemAll' .nextflow.log` == 3 ]] || false
[[ `grep -c 'p1.fa p2.fa' .stdout` == 1 ]] || false
[[ `grep -c 'p3.fa p4.fa' .stdout` == 1 ]] || false
[[ `grep -c 'p5.fa' .stdout` == 1 ]] || false
#
# run resume mode
#
$NXF_RUN -resume | tee .stdout
[[ `grep -c 'Cached process > blastThemAll' .nextflow.log` == 3 ]] || false
[[ `grep -c 'p1.fa p2.fa' .stdout` == 1 ]] || false
[[ `grep -c 'p3.fa p4.fa' .stdout` == 1 ]] || false
[[ `grep -c 'p5.fa' .stdout` == 1 ]] || false

42
nextflow/tests-v1/checks/cache-bak.nf/.checks Normal file
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set -e
# Skip test if AWS keys are missing
if [[ ! $AWS_ACCESS_KEY_ID ]]; then
echo "Skip cache-bak test since AWS keys are not available"
exit 0
fi
#
# setup env
#
export NXF_IGNORE_RESUME_HISTORY=true
export NXF_UUID=$(uuidgen | tr [:upper:] [:lower:])
#
# run normal mode
#
$NXF_RUN -name test_1 | tee .stdout
[[ `grep -c 'Submitted process > foo' .nextflow.log` == 1 ]] || false
#
# backup cache
#
NXF_WORK=s3://nextflow-ci/cache-test \
$NXF_CMD -log .nextflow-backup.log plugin nf-tower:cache-backup
#
# remove it
#
rm -rf .nextflow
#
# restore cache
#
NXF_WORK=s3://nextflow-ci/cache-test \
$NXF_CMD -log .nextflow-restore.log plugin nf-tower:cache-restore
#
# run resume mode
#
$NXF_RUN -name test_2 -resume $NXF_UUID | tee .stdout
[[ `grep -c 'Cached process > foo' .nextflow.log` == 1 ]] || false

15
nextflow/tests-v1/checks/chunk.nf/.checks Normal file
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@@ -0,0 +1,15 @@
set -e
#
# run normal mode
#
$NXF_RUN --chunkSize 3 < .data.fa | tee .stdout
[[ `grep -c 'Submitted process > foo' .nextflow.log` == 2 ]] || false
#
# run resume mode
#
$NXF_RUN -resume --chunkSize 3 < .data.fa | tee .stdout
[[ `grep -c 'Cached process > foo' .nextflow.log` == 2 ]] || false

14
nextflow/tests-v1/checks/chunk.nf/.data.fa Normal file
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@@ -0,0 +1,14 @@
>1aboA
NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPS
NYITPVN
>1ycsB
KGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGY
VPRNLLGLYP
>1pht
GYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIG
WLNGYNETTGERGDFPGTYVEYIGRKKISP
>1vie
DRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERI
N
>1ihvA
NFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD

35
nextflow/tests-v1/checks/cli-args.nf/.checks Normal file
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set -e
#
# run normal mode
#
echo ''
$NXF_RUN --alpha uno --beta \* --delta 'x_{1,2}.fasta' --gamma hello\ world --omega '--foo bar' a b c | tee stdout
< stdout grep -F 'alpha: uno'
< stdout grep -F 'beta : *'
< stdout grep -F 'delta: x_{1,2}.fasta'
< stdout grep -F 'gamma: hello world'
< stdout grep -F 'omega: --foo bar'
< stdout grep -F 'args : a_b_c'
#
# check quotes
#
echo ''
$NXF_RUN --alpha "a'b" --beta 'a"b' --delta 'x' --gamma "x" --omega x "a b c" | tee stdout
< stdout grep -F "alpha: a'b"
< stdout grep -F 'beta : a"b'
< stdout grep -F 'delta: x'
< stdout grep -F 'gamma: x'
< stdout grep -F 'omega: x'
< stdout grep -F 'args : a b c'
#
# check the log command handle properly quoted filter options
#
$NXF_CMD -log .nextflow.log log last -F 'container = "ubuntu"' | tee log
[[ $? == 0 ]] || exit 1
$NXF_CMD -log .nextflow.log log last -F "container = 'ubuntu'" | tee log
[[ $? == 0 ]] || exit 1

20
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# Skip test if AWS keys are missing
if [ -z "$AWS_ACCESS_KEY_ID" ]; then
echo "Missing AWS credentials -- Skipping test"
exit 0
fi
## random file name
NAME=test-cmd-$(basename `mktemp`).file
## create random file
head -c 1000000 </dev/urandom >myfile
## upload it
$NXF_CMD -log cmd-fs-1.log fs cp myfile s3://nextflow-ci/$NAME
## download it
$NXF_CMD -log cmd-fs-2.log fs cp s3://nextflow-ci/$NAME $NAME
## check they are equals
diff myfile $NAME || false

8
nextflow/tests-v1/checks/collect-file.nf/.checks Normal file
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echo ''
echo \$ $NXF_RUN
$NXF_RUN | tee stdout
[[ `<stdout grep -c 'Entries are saved to file'` == 1 ]] || false
[[ `<stdout grep -c 'alpha'` == 1 ]] || false
[[ `<stdout grep -c 'beta'` == 1 ]] || false
[[ `<stdout grep -c 'gamma'` == 1 ]] || false

34
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set -e
#
# run normal mode
#
echo ''
echo \$ $NXF_RUN
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > algn'` == 6 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > merge'` == 2 ]] || false
[[ `grep -c 'barcode: alpha' stdout` == 1 ]] || false
[[ `grep -c 'barcode: gamma' stdout` == 1 ]] || false
[[ `grep -c 'bam : bam1 bam2 bam3' stdout` == 2 ]] || false
[[ `grep -c 'bai : bai1 bai2 bai3' stdout` == 2 ]] || false
[[ `grep -c 'seq_ids' stdout` == 2 ]] || false
#
# RESUME mode
#
echo ''
echo \$ $NXF_RUN -resume
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > algn'` == 6 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > merge'` == 2 ]] || false
[[ `grep -c 'barcode: alpha' stdout` == 1 ]] || false
[[ `grep -c 'barcode: gamma' stdout` == 1 ]] || false
[[ `grep -c 'bam : bam1 bam2 bam3' stdout` == 2 ]] || false
[[ `grep -c 'bai : bai1 bai2 bai3' stdout` == 2 ]] || false
[[ `grep -c 'seq_ids' stdout` == 2 ]] || false

44
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set -e
#
# basic run
#
echo ''
$NXF_RUN > stdout
[[ `<stdout grep -c 'Hello world!'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > bar'` == 1 ]] || false
( cd foo;
[[ -s f1.fa ]] || false
[[ -s f2.fa ]] || false
[[ -s f3.fa ]] || false
[[ -s hello.txt ]] || false
[[ -s sample.zip ]] || false
[[ -s sample.html ]] || false
[[ -s '01_A(R1).fastq' ]] || false
[[ -s '01_A(R2).fastq' ]] || false
[[ -s 'sample_(1 2).vcf' ]] || false
[[ -s .alpha/hello.txt ]] || false
)
#
# resume
#
rm -rf foo
echo ''
$NXF_RUN -resume > stdout
[[ `<stdout grep -c 'Hello world!'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > bar'` == 1 ]] || false
( cd foo;
[[ -s f1.fa ]] || false
[[ -s f2.fa ]] || false
[[ -s f3.fa ]] || false
[[ -s hello.txt ]] || false
[[ -s sample.zip ]] || false
[[ -s sample.html ]] || false
[[ -s '01_A(R1).fastq' ]] || false
[[ -s '01_A(R2).fastq' ]] || false
[[ -s 'sample_(1 2).vcf' ]] || false
[[ -s .alpha/hello.txt ]] || false
)

39
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# apply labels for profile `test1`
$NXF_RUN -c ../../config-labels.config -profile test1 | tee stdout
< stdout grep "alpha memry: 20 MB" || false
< stdout grep "alpha queue: std" || false
< stdout grep "beta memry: 10 MB" || false
< stdout grep "beta queue: small" || false
< stdout grep "delta memry: 70 MB" || false
< stdout grep "delta queue: big" || false
< stdout grep "gamma memry: 70 MB" || false
< stdout grep "gamma queue: big" || false
# apply labels for profile `test2`
$NXF_RUN -c ../../config-labels.config -profile test2 | tee stdout
< stdout grep "beta memry: 10 MB" || false
< stdout grep "beta queue: small" || false
< stdout grep "alpha memry: 70 MB" || false
< stdout grep "alpha queue: big" || false
< stdout grep "delta memry: 70 MB" || false
< stdout grep "delta queue: big" || false
< stdout grep "gamma memry: 70 MB" || false
< stdout grep "gamma queue: big" || false
# apply labels for profile `test3`
$NXF_RUN -c ../../config-labels.config -profile test3 | tee stdout
< stdout grep "beta memry: 50 MB" || false
< stdout grep "beta queue: all" || false
< stdout grep "alpha memry: 50 MB" || false
< stdout grep "alpha queue: all" || false
< stdout grep "delta memry: 50 MB" || false
< stdout grep "delta queue: all" || false
< stdout grep "gamma memry: 60 MB" || false
< stdout grep "gamma queue: foo" || false

20
nextflow/tests-v1/checks/config-vars.nf/.checks Normal file
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#
# run normal mode
#
$NXF_RUN -c ../../config-vars.config | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 2 ]] || false
< stdout grep "foo 1,2" || false
< stdout grep "bar 3,4" || false
#
# run resume mode
#
$NXF_RUN -c ../../config-vars.config -resume | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 2 ]] || false
< stdout grep "foo 1,2" || false
< stdout grep "bar 3,4" || false

21
nextflow/tests-v1/checks/copy-no-follow.nf/.checks Normal file
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set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process '` == 1 ]] || false
[[ -f outputDir/testFile.txt ]] || false
[[ -L outputDir/testFileLink.txt ]] || false
#
# run resume mode
#
rm -rf outputDir
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process '` == 1 ]] || false
[[ -f outputDir/testFile.txt ]] || false
[[ -L outputDir/testFileLink.txt ]] || false

23
nextflow/tests-v1/checks/custom-lib.nf/.checks Normal file
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#
# check the ability to load custom script/classes in the
# local `lib` directory
#
set -e
# copy the test script in this directory
cp ${NXF_SCRIPT:-../../custom-lib.nf} test.nf
# crate a library class
mkdir -p lib
cat >lib/Foo.groovy <<EOL
class Foo {
static String hello() { "Hello world!" }
}
EOL
${NXF_CMD:-nextflow} run test.nf | tee stdout
[[ `< stdout grep -c 'Hello world!'` == 1 ]] || false

32
nextflow/tests-v1/checks/demo.nf/.checks Normal file
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set -e
#
# run normal mode
#
echo ''
echo \$ $NXF_RUN
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > sayHello'` == 5 ]] || false
[[ `grep 'Hola world!' stdout` ]] || false
[[ `grep 'Γεια σου world!' stdout` ]] || false
[[ `grep 'Hello world!' stdout` ]] || false
[[ `grep 'Bojour world!' stdout` ]] || false
[[ `grep 'Ciao world!' stdout` ]] || false
#
# RESUME mode
#
echo ''
echo \$ $NXF_RUN -resume
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > sayHello'` == 5 ]] || false
[[ `grep 'Hola world!' stdout` ]] || false
[[ `grep 'Γεια σου world!' stdout` ]] || false
[[ `grep 'Hello world!' stdout` ]] || false
[[ `grep 'Bojour world!' stdout` ]] || false
[[ `grep 'Ciao world!' stdout` ]] || false

2
nextflow/tests-v1/checks/dyn-mem.nf/.big.txt Normal file
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1234567890
1234567890

18
nextflow/tests-v1/checks/dyn-mem.nf/.checks Normal file
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@@ -0,0 +1,18 @@
set -e
#
# run normal mode
#
$NXF_RUN -process.debug | tee stdout
[[ `< .nextflow.log grep -c 'Submitted process'` == 2 ]] || false
[[ `< stdout grep 'task=.small.txt mem=100 MB'` ]] || false
[[ `< stdout grep 'task=.big.txt mem=200 MB'` ]] || false
#
# run resume mode
#
$NXF_RUN -process.debug -resume | tee stdout
[[ `< .nextflow.log grep -c 'Cached process'` == 2 ]] || false

1
nextflow/tests-v1/checks/dyn-mem.nf/.small.txt Normal file
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@@ -0,0 +1 @@
12345

45
nextflow/tests-v1/checks/dynamic-filename.nf/.checks Normal file
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@@ -0,0 +1,45 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 4 ]] || false
grep '~ Saving my_delta.txt' stdout
grep '~ Saving my_omega.txt' stdout
grep '~ Saving my_gamma.txt' stdout
grep '~ Saving my_alpha.txt' stdout
test -f my_alpha.txt
test -f my_delta.txt
test -f my_gamma.txt
test -f my_omega.txt
diff my_alpha.txt .expected
diff my_delta.txt .expected
diff my_gamma.txt .expected
diff my_omega.txt .expected
rm my_*
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 4 ]] || false
grep '~ Saving my_delta.txt' stdout
grep '~ Saving my_omega.txt' stdout
grep '~ Saving my_gamma.txt' stdout
grep '~ Saving my_alpha.txt' stdout
test -f my_alpha.txt
test -f my_delta.txt
test -f my_gamma.txt
test -f my_omega.txt

2
nextflow/tests-v1/checks/dynamic-filename.nf/.expected Normal file
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@@ -0,0 +1,2 @@
Hello
World

76
nextflow/tests-v1/checks/dynamic-storedir.nf/.checks Normal file
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set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 4 ]] || false
grep "Result $PWD/cache/omega/result.txt" stdout
grep "Result $PWD/cache/delta/result.txt" stdout
grep "Result $PWD/cache/alpha/result.txt" stdout
grep "Result $PWD/cache/gamma/result.txt" stdout
test -f my_alpha.txt
test -f my_delta.txt
test -f my_gamma.txt
test -f my_omega.txt
diff my_alpha.txt .expected
diff my_delta.txt .expected
diff my_gamma.txt .expected
diff my_omega.txt .expected
rm my_*
#
# run normal mode -- this time store result are used
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -E -c '\[skipping\] Stored process > foo'` == 4 ]] || false
grep "Result $PWD/cache/omega/result.txt" stdout
grep "Result $PWD/cache/delta/result.txt" stdout
grep "Result $PWD/cache/alpha/result.txt" stdout
grep "Result $PWD/cache/gamma/result.txt" stdout
test -f my_alpha.txt
test -f my_delta.txt
test -f my_gamma.txt
test -f my_omega.txt
diff my_alpha.txt .expected
diff my_delta.txt .expected
diff my_gamma.txt .expected
diff my_omega.txt .expected
rm my_*
#
# run resume mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -E -c '\[skipping\] Stored process > foo'` == 4 ]] || false
grep "Result $PWD/cache/omega/result.txt" stdout
grep "Result $PWD/cache/delta/result.txt" stdout
grep "Result $PWD/cache/alpha/result.txt" stdout
grep "Result $PWD/cache/gamma/result.txt" stdout
test -f my_alpha.txt
test -f my_delta.txt
test -f my_gamma.txt
test -f my_omega.txt
diff my_alpha.txt .expected
diff my_delta.txt .expected
diff my_gamma.txt .expected
diff my_omega.txt .expected

2
nextflow/tests-v1/checks/dynamic-storedir.nf/.expected Normal file
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@@ -0,0 +1,2 @@
Hello
World

35
nextflow/tests-v1/checks/each-file.nf/.checks Normal file
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@@ -0,0 +1,35 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo (p1.fa)'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo (p2.fa)'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo (p3.fa)'` == 1 ]] || false
[[ `< stdout grep -c '>1ycsB'` == 2 ]] || false
[[ `< stdout grep -c '>1pht'` == 2 ]] || false
[[ `< stdout grep -c '>1aboA'` == 1 ]] || false
[[ `< stdout grep -c '>1ihvA'` == 1 ]] || false
[[ `< stdout grep -c '>1vie'` == 1 ]] || false
#
# run resume mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo (p1.fa)'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo (p2.fa)'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo (p3.fa)'` == 1 ]] || false
[[ `< stdout grep -c '>1ycsB'` == 2 ]] || false
[[ `< stdout grep -c '>1pht'` == 2 ]] || false
[[ `< stdout grep -c '>1aboA'` == 1 ]] || false
[[ `< stdout grep -c '>1ihvA'` == 1 ]] || false
[[ `< stdout grep -c '>1vie'` == 1 ]] || false

77
nextflow/tests-v1/checks/env-container-with(special)chars.nf/.checks Normal file
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@@ -0,0 +1,77 @@
set -e
export NXF_ANSI_LOG=false
#
# create the `hello.sh` executable script
#
mkdir -p bin
echo "echo Hola mundo" > bin/hello.sh
chmod +x bin/hello.sh
#
# create the nextflow config file
#
cat << EOF > nextflow.config
env.FOO = 'HOLA'
process.container = 'quay.io/nextflow/bash'
EOF
#
# create the nextflow script
#
cat << EOF > foo.nf
process foo {
echo true
input:
env BAR
'''
env | grep -E "^(FOO|BAR)" | sort
hello.sh
'''
}
workflow {
channel.value('Hello World!') | foo
}
EOF
#
# not the testing part
#
# NF plain run
$NXF_CMD run foo.nf | tee stdout
# run tests
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
# NF run with trace
$NXF_CMD run foo.nf -with-trace | tee stdout
# run tests
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
# NF run with docker
$NXF_CMD run foo.nf -with-docker | tee stdout
# run tests
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
# NF run with docker and trace
$NXF_CMD run foo.nf -with-trace -with-docker | tee stdout
# run tests
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false

77
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set -e
export NXF_ANSI_LOG=false
#
# create the `hello.sh` executable script
#
mkdir -p bin
echo "echo Hola mundo" > bin/hello.sh
chmod +x bin/hello.sh
#
# create the nextflow config file
#
cat << EOF > nextflow.config
env.FOO = 'HOLA'
process.container = 'quay.io/nextflow/bash'
EOF
#
# create the nextflow script
#
cat << EOF > foo.nf
process foo {
echo true
input:
env BAR
'''
env | grep -E "^(FOO|BAR)" | sort
hello.sh
'''
}
workflow {
channel.value('Hello World!') | foo
}
EOF
#
# not the testing part
#
# NF plain run
$NXF_CMD run foo.nf | tee stdout
# run tests
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
# NF run with trace
$NXF_CMD run foo.nf -with-trace | tee stdout
# run tests
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
# NF run with docker
$NXF_CMD run foo.nf -with-docker | tee stdout
# run tests
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
# NF run with docker and trace
$NXF_CMD run foo.nf -with-trace -with-docker | tee stdout
# run tests
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false

17
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@@ -0,0 +1,17 @@
#
# run normal mode
#
$NXF_RUN | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 2 ]] || false
[[ `< .stdout grep 'bar says Hello'` ]] || false
#
# run resume mode
#
$NXF_RUN -resume | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 2 ]] || false
[[ `< .stdout grep 'bar says Hello'` ]] || false

21
nextflow/tests-v1/checks/error-finish.nf/.checks Normal file
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set -e
export NXF_ASSETS=$PWD/assets
#
# First run test `success` is `true`
#
set +e
echo ''
$NXF_RUN > stdout
status=$?
set -e
# the exit status must NOT be zero because the pipeline throws an error
[ $status -ne 0 ] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 3 ]] || false
[[ `grep -c 'success: false' stdout` == 1 ]] || false
[[ `grep -c 'exitStatus: 99' stdout` == 1 ]] || false
[[ `grep -c 'run_1' stdout` == 1 ]] || false
[[ `grep -c 'run_2' stdout` == 1 ]] || false

13
nextflow/tests-v1/checks/error-ignore-then-fail.nf/.checks Normal file
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@@ -0,0 +1,13 @@
set -e
set +e
echo ''
$NXF_CMD -q run $NXF_SCRIPT -c .config > stdout
status=$?
set -e
[ $status -ne 0 ] || false
[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 3 ]] || false
[[ `< .nextflow.log grep -c 'Submitted process > bar'` == 1 ]] || false
[[ `< .nextflow.log grep -c 'Error is ignored'` == 1 ]] || false

6
nextflow/tests-v1/checks/error-ignore-then-fail.nf/.config Normal file
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@@ -0,0 +1,6 @@
workflow {
failOnIgnore = true
}
process {
errorStrategy = 'ignore'
}

6
nextflow/tests-v1/checks/error-message.nf/.checks Normal file
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@@ -0,0 +1,6 @@
set +e
$NXF_RUN | tee stdout
set -e
< stdout grep "Check script '.*error-message.nf' at line: 19"

23
nextflow/tests-v1/checks/error.nf/.checks Normal file
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@@ -0,0 +1,23 @@
set -e
#
# run normal mode
#
$NXF_RUN -c .config | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > task1'` == 3 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > task2'` == 3 ]] || false
[[ `grep 'NOTE' .nextflow.log | grep -E -c "Process .* terminated with an error exit status"` == 3 ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -c .config -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > task1'` == 3 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > task2'` == 3 ]] || false
[[ `grep 'NOTE' .nextflow.log | grep -E -c "Process .* terminated with an error exit status"` == 3 ]] || false

1
nextflow/tests-v1/checks/error.nf/.config Normal file
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@@ -0,0 +1 @@
process.errorStrategy = { task.exitStatus >= 1 ? 'retry' : 'ignore' }

24
nextflow/tests-v1/checks/escape-globs.nf/.checks Normal file
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set -e
mkdir \[work-dir\]
#
# run normal mode
#
$NXF_RUN -w \[work-dir\] | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
[[ `< stdout grep -c -F 'match: file[a-b].txt'` == 1 ]] || false
[[ `< stdout grep -c -F 'match: file-*.txt'` == 1 ]] || false
[[ `< stdout grep -c -F 'match: file-?.txt'` == 1 ]] || false
#
# run resume mode
#
$NXF_RUN -w \[work-dir\] -resume | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 1 ]] || false
[[ `< stdout grep -c -F 'match: file[a-b].txt'` == 1 ]] || false
[[ `< stdout grep -c -F 'match: file-*.txt'` == 1 ]] || false
[[ `< stdout grep -c -F 'match: file-?.txt'` == 1 ]] || false

17
nextflow/tests-v1/checks/eval-out.nf/.checks Normal file
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@@ -0,0 +1,17 @@
#
# run normal mode
#
$NXF_RUN | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
[[ `< .stdout grep 'GNU bash'` ]] || false
#
# run resume mode
#
$NXF_RUN -resume | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 1 ]] || false
[[ `< .stdout grep 'GNU bash'` ]] || false

10
nextflow/tests-v1/checks/exit-if-empty.nf/.checks Normal file
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@@ -0,0 +1,10 @@
set +e
set -o pipefail
echo ''
echo \$ $NXF_RUN
$NXF_RUN | tee stdout
# must return a non-zero exit status
[[ $? == 0 ]] && exit 1
[[ `<stdout grep -c 'Channel empty terminating'` == 1 ]] || false

18
nextflow/tests-v1/checks/exitstatus-fail.nf/.checks Normal file
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@@ -0,0 +1,18 @@
set +e
#
# run normal mode
#
echo ''
$NXF_RUN
[[ $? == 0 ]] && exit 1
#
# RESUME mode
#
echo ''
$NXF_RUN -resume
[[ $? == 0 ]] && exit 1
exit 0

21
nextflow/tests-v1/checks/fair.nf/.checks Normal file
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@@ -0,0 +1,21 @@
set -e
export NXF_ANSI_LOG=false
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 26 ]] || false
cmp stdout .expected || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 26 ]] || false
cmp stdout .expected || false

26
nextflow/tests-v1/checks/fair.nf/.expected Normal file
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@@ -0,0 +1,26 @@
[1, a]
[2, b]
[3, c]
[4, d]
[5, e]
[6, f]
[7, g]
[8, h]
[9, i]
[10, j]
[11, k]
[12, l]
[13, m]
[14, n]
[15, o]
[16, p]
[17, q]
[18, r]
[19, s]
[20, t]
[21, u]
[22, v]
[23, w]
[24, x]
[25, y]
[26, z]

20
nextflow/tests-v1/checks/file-with-blanks.nf/.checks Normal file
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@@ -0,0 +1,20 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 1 ]] || false
[[ `< stdout grep -c 'Hello' ` == 1 ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `< .nextflow.log grep -c 'Cached process > foo'` == 1 ]] || false
[[ `< stdout grep -c 'Hello' ` == 1 ]] || false

20
nextflow/tests-v1/checks/file-with-quote.nf/.checks Normal file
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@@ -0,0 +1,20 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 1 ]] || false
[[ `< stdout grep -c 'Hello' ` == 1 ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `< .nextflow.log grep -c 'Cached process > foo'` == 1 ]] || false
[[ `< stdout grep -c 'Hello' ` == 1 ]] || false

25
nextflow/tests-v1/checks/files.nf/.checks Normal file
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@@ -0,0 +1,25 @@
set -e
#
# run normal mode
#
echo ''
echo \$ $NXF_RUN
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > split'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > printTwo'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > printLast'` == 2 ]] || false
#
# RESUME mode
#
echo ''
echo \$ $NXF_RUN -resume
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > split'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > printTwo'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > printLast'` == 2 ]] || false

27
nextflow/tests-v1/checks/fusion-symlink.nf/.checks Normal file
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@@ -0,0 +1,27 @@
#!/bin/bash
# Skip test if AWS keys are missing
if [ -z "$AWS_ACCESS_KEY_ID" ]; then
echo "Missing AWS credentials -- Skipping test"
exit 0
fi
OUTDIR="s3://nextflow-ci/work/ci-test/fusion-symlink/$(uuidgen)"
#
# normal run
#
echo initial run
$NXF_RUN -c .config --outdir "$OUTDIR"
$NXF_CMD fs cp "$OUTDIR/data.txt" data.txt
cmp data.txt .expected || false
#
# resume run
#
echo resumed run
$NXF_RUN -c .config --outdir "$OUTDIR" -resume
$NXF_CMD fs cp "$OUTDIR/data.txt" data.txt
cmp data.txt .expected || false

5
nextflow/tests-v1/checks/fusion-symlink.nf/.config Normal file
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@@ -0,0 +1,5 @@
workDir = 's3://nextflow-ci/work'
fusion.enabled = true
fusion.exportStorageCredentials = true
wave.enabled = true
docker.runOptions = '-e FUSION_TRACING_DESTINATION=objectstore://'

1
nextflow/tests-v1/checks/fusion-symlink.nf/.expected Normal file
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@@ -0,0 +1 @@
HELLO

27
nextflow/tests-v1/checks/glob.nf/.checks Normal file
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@@ -0,0 +1,27 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > recurseDir'` == 1 ]] || false
grep 'result1: file2.fa' stdout
grep 'result1: file3.fa' stdout
grep 'result1: file4.fa' stdout
grep 'result2: file5.txt' stdout
#
# run resume mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > recurseDir'` == 1 ]] || false
grep 'result1: file2.fa' stdout
grep 'result1: file3.fa' stdout
grep 'result1: file4.fa' stdout
grep 'result2: file5.txt' stdout

31
nextflow/tests-v1/checks/hello.nf/.checks Normal file
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@@ -0,0 +1,31 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > sayhello'` == 1 ]] || false
[[ `grep -c 'Hello world!' stdout` == 1 ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > sayhello'` == 1 ]] || false
[[ `grep -c 'Hello world!' stdout` == 1 ]] || false
#
# checks reports
#
echo ''
$NXF_RUN -with-report -with-timeline -with-trace -with-dag | tee stdout
[ -s report-*.html ] || false
[ -s timeline-*.html ] || false
[ -s trace-*.txt ] || false
[ -s dag-*.html ] || false

28
nextflow/tests-v1/checks/input.nf/.checks Normal file
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@@ -0,0 +1,28 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 2 ]] || false
[[ `grep -c '1 - a' stdout` == 1 ]] || false
[[ `grep -c '1 - b' stdout` == 1 ]] || false
[[ `grep -c 'foo out: a' stdout` == 1 ]] || false
[[ `grep -c 'foo out: b' stdout` == 1 ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 2 ]] || false
[[ `grep -c '1 - a' stdout` == 1 ]] || false
[[ `grep -c '1 - b' stdout` == 1 ]] || false
[[ `grep -c 'foo out: a' stdout` == 1 ]] || false
[[ `grep -c 'foo out: b' stdout` == 1 ]] || false

21
nextflow/tests-v1/checks/mixing-langs.nf/.checks Normal file
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@@ -0,0 +1,21 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > perlTask'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > pyTask'` == 1 ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > perlTask'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > pyTask'` == 1 ]] || false

1
nextflow/tests-v1/checks/mixing-langs.nf/.expected Normal file
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@@ -0,0 +1 @@
avg: 43.5159945284 - 36.8211561596

20
nextflow/tests-v1/checks/nativeCode.nf/.checks Normal file
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@@ -0,0 +1,20 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > nativeCode'` == 1 ]] || false
grep 'Hello world' stdout
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > nativeCode'` == 1 ]] || false
grep 'Hello world' stdout

18
nextflow/tests-v1/checks/opt-file.nf/.checks Normal file
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@@ -0,0 +1,18 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 1 ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `< .nextflow.log grep -c 'Cached process > foo'` == 1 ]] || false

78
nextflow/tests-v1/checks/output-dsl.nf/.checks Normal file
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@@ -0,0 +1,78 @@
#
# run normal mode
#
echo First run
$NXF_RUN --save_bam_bai | tee stdout
[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > fastqc') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > align') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > quant') == 3 ]] || false
[[ -f results/log/alpha.fastqc.log ]] || false
[[ -f results/log/beta.fastqc.log ]] || false
[[ -f results/log/delta.fastqc.log ]] || false
[[ -f results/align/alpha.bai ]] || false
[[ -f results/align/alpha.bam ]] || false
[[ -f results/align/beta.bai ]] || false
[[ -f results/align/beta.bam ]] || false
[[ -f results/align/delta.bai ]] || false
[[ -f results/align/delta.bam ]] || false
[[ -L results/quant/alpha ]] || false
[[ -L results/quant/beta ]] || false
[[ -L results/quant/delta ]] || false
[[ -f results/samples.csv ]] || false
[[ -f results/summary.txt ]] || false
#
# one more time to make sure 'overwrite' is fine
#
echo Second run
$NXF_RUN --save_bam_bai | tee stdout
[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > fastqc') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > align') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > quant') == 3 ]] || false
[[ -f results/log/alpha.fastqc.log ]] || false
[[ -f results/log/beta.fastqc.log ]] || false
[[ -f results/log/delta.fastqc.log ]] || false
[[ -f results/align/alpha.bai ]] || false
[[ -f results/align/alpha.bam ]] || false
[[ -f results/align/beta.bai ]] || false
[[ -f results/align/beta.bam ]] || false
[[ -f results/align/delta.bai ]] || false
[[ -f results/align/delta.bam ]] || false
[[ -L results/quant/alpha ]] || false
[[ -L results/quant/beta ]] || false
[[ -L results/quant/delta ]] || false
[[ -f results/samples.csv ]] || false
[[ -f results/summary.txt ]] || false
#
# clean & run resume mode
#
echo Third run
rm -rf results
$NXF_RUN --save_bam_bai -resume | tee stdout
[[ $(grep INFO .nextflow.log | grep -c 'Cached process > fastqc') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Cached process > align') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Cached process > quant') == 3 ]] || false
[[ -f results/log/alpha.fastqc.log ]] || false
[[ -f results/log/beta.fastqc.log ]] || false
[[ -f results/log/delta.fastqc.log ]] || false
[[ -f results/align/alpha.bai ]] || false
[[ -f results/align/alpha.bam ]] || false
[[ -f results/align/beta.bai ]] || false
[[ -f results/align/beta.bam ]] || false
[[ -f results/align/delta.bai ]] || false
[[ -f results/align/delta.bam ]] || false
[[ -L results/quant/alpha ]] || false
[[ -L results/quant/beta ]] || false
[[ -L results/quant/delta ]] || false
[[ -f results/samples.csv ]] || false
[[ -f results/summary.txt ]] || false

25
nextflow/tests-v1/checks/output-file.nf/.checks Normal file
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@@ -0,0 +1,25 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
[[ `< stdout grep 'dummy'` ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 1 ]] || false
[[ `< stdout grep 'dummy'` ]] || false

28
nextflow/tests-v1/checks/output-globs.nf/.checks Normal file
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@@ -0,0 +1,28 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > bar'` == 1 ]] || false
[[ `< stdout grep -E 'foo.*/a/a/2\.txt' ` ]] || false
[[ `< stdout grep -E 'bar.*/a/a/2\.txt' ` ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > bar'` == 1 ]] || false
[[ `< stdout grep -E 'foo.*/a/a/2\.txt' ` ]] || false
[[ `< stdout grep -E 'bar.*/a/a/2\.txt' ` ]] || false

18
nextflow/tests-v1/checks/output-links.nf/.checks Normal file
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@@ -0,0 +1,18 @@
set -e
#
# run normal mode
#
$NXF_RUN -process.scratch true | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
#
# run resume mode
#
$NXF_RUN -resume -process.scratch true | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 1 ]] || false

30
nextflow/tests-v1/checks/output-val.nf/.checks Normal file
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@@ -0,0 +1,30 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
[[ `< stdout grep 'x: 100'` ]] || false
[[ `< stdout grep 'y: two hundred'` ]] || false
[[ `< stdout grep 'str: Hello'` ]] || false
[[ `< stdout grep 'exp: prot-100.out'` ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 1 ]] || false
[[ `< stdout grep 'x: 100'` ]] || false
[[ `< stdout grep 'y: two hundred'` ]] || false
[[ `< stdout grep 'str: Hello'` ]] || false
[[ `< stdout grep 'exp: prot-100.out'` ]] || false

4
nextflow/tests-v1/checks/print-http-file.nf/.checks Normal file
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@@ -0,0 +1,4 @@
$NXF_RUN | tee stdout
[[ `< stdout grep -c 'User-agent'` != 0 ]] || false
[[ `< stdout grep -c 'Disallow'` != 0 ]] || false

16
nextflow/tests-v1/checks/process-arity.nf/.checks Normal file
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@@ -0,0 +1,16 @@
set +e
#
# run normal mode
#
echo ''
$NXF_RUN
[[ $? == 0 ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume
[[ $? == 0 ]] || false

43
nextflow/tests-v1/checks/profiles.nf/.checks Normal file
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@@ -0,0 +1,43 @@
#
# verify default profile
#
$NXF_CMD -C ../../profiles.config config | tee stdout
cmp stdout .expected_profile_standard.txt || false
#
# verify advanced profile
#
$NXF_CMD -C ../../profiles.config config -profile advanced | tee stdout
cmp stdout .expected_profile_advanced.txt || false
#
# verify *all* profile
#
$NXF_CMD -C ../../profiles.config config -a | tee stdout
cmp stdout .expected_profile_all.txt || false
#
# verify return error
#
$NXF_CMD -C ../../profiles.config config -profile xxx 2>&1| tee stdout
[[ ${PIPESTATUS[0]} == 0 ]] && exit 1
< stdout grep "Unknown configuration profile: 'xxx'" || false
#
# Verify run uses the default profile
#
$NXF_CMD -C ../../profiles.config run $NXF_SCRIPT | tee stdout
< stdout grep "cpus: 2 memory: 2 GB" || false
#
# Verify run uses the *advanced* profile
#
$NXF_CMD -C ../../profiles.config run $NXF_SCRIPT -profile advanced | tee stdout
< stdout grep "cpus: 8 memory: 10 GB" || false
#
# Verify that return an error code
#
$NXF_CMD -C ../../profiles.config run $NXF_SCRIPT -profile foo 2>&1| tee stdout
[[ ${PIPESTATUS[0]} == 0 ]] && exit 1
< stdout grep "Unknown configuration profile: 'foo'" || false

8
nextflow/tests-v1/checks/profiles.nf/.expected_profile_advanced.txt Normal file
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@@ -0,0 +1,8 @@
echo = true
foo = 'bar'
process {
cpus = 8
memory = '10GB'
disk = '300GB'
}

18
nextflow/tests-v1/checks/profiles.nf/.expected_profile_all.txt Normal file
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@@ -0,0 +1,18 @@
echo = true
foo = 'bar'
profiles {
standard {
process {
cpus = 2
memory = '2GB'
}
}
advanced {
process {
cpus = 8
memory = '10GB'
disk = '300GB'
}
}
}

7
nextflow/tests-v1/checks/profiles.nf/.expected_profile_standard.txt Normal file
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@@ -0,0 +1,7 @@
echo = true
foo = 'bar'
process {
cpus = 2
memory = '2GB'
}

10
nextflow/tests-v1/checks/property-out-vals.nf/.checks Normal file
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@@ -0,0 +1,10 @@
$NXF_RUN | tee stdout
[[ `< stdout grep -c 'exit_status=0'` != 0 ]] || false
[[ `< stdout grep -c 'record=aaa_bbb'` != 0 ]] || false
$NXF_RUN -resume | tee stdout
[[ `< stdout grep -c 'exit_status=0'` != 0 ]] || false
[[ `< stdout grep -c 'record=aaa_bbb'` != 0 ]] || false

73
nextflow/tests-v1/checks/publish-dir.nf/.checks Normal file
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@@ -0,0 +1,73 @@
#
# run normal mode
#
echo First run
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > align'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > my_combine'` == 1 ]] || false
cmp stdout .expected || false
[[ -f data/alpha.bai ]] || false
[[ -f data/alpha.bam ]] || false
[[ -f data/beta.bai ]] || false
[[ -f data/beta.bam ]] || false
[[ -f data/delta.bai ]] || false
[[ -f data/delta.bam ]] || false
[[ -L data/result.txt ]] || false
[[ -f more/data/result.txt ]] || false
[[ -f data/xxx/A ]] || false
[[ -f data/xxx/B ]] || false
[[ -f data/xxx/C ]] || false
#
# one more time to make sure 'overwrite' is fine
#
echo Second run
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > align'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > my_combine'` == 1 ]] || false
cmp stdout .expected || false
[[ -f data/alpha.bai ]] || false
[[ -f data/alpha.bam ]] || false
[[ -f data/beta.bai ]] || false
[[ -f data/beta.bam ]] || false
[[ -f data/delta.bai ]] || false
[[ -f data/delta.bam ]] || false
[[ -L data/result.txt ]] || false
[[ -f more/data/result.txt ]] || false
[[ -f data/xxx/A ]] || false
[[ -f data/xxx/B ]] || false
[[ -f data/xxx/C ]] || false
#
# clean & run resume mode
#
echo Third run
rm -rf data
rm -rf more/data
$NXF_RUN -resume | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process > align'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > my_combine'` == 1 ]] || false
cmp stdout .expected || false
[[ -f data/alpha.bai ]] || false
[[ -f data/alpha.bam ]] || false
[[ -f data/beta.bai ]] || false
[[ -f data/beta.bam ]] || false
[[ -f data/delta.bai ]] || false
[[ -f data/delta.bam ]] || false
[[ -L data/result.txt ]] || false
[[ -f more/data/result.txt ]] || false
#
# NOTE: on Mac when deleting an hard-link also the origin is removed
#
[[ -f data/xxx/A ]] || false
[[ -f data/xxx/B ]] || false
[[ -f data/xxx/C ]] || false

7
nextflow/tests-v1/checks/publish-dir.nf/.expected Normal file
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@@ -0,0 +1,7 @@
alpha
beta
delta
ahpla
ateb
atled

20
nextflow/tests-v1/checks/publish-nested.nf/.checks Normal file
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@@ -0,0 +1,20 @@
#
# run normal mode
#
echo First run
$NXF_RUN --x ciao | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
[[ $(cat data/a/b/c/file.txt) == ciao ]] || false
#
# second run, must overwrite the file
#
echo First run
$NXF_RUN --x miao | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
[[ $(cat data/a/b/c/file.txt) == miao ]] || false

30
nextflow/tests-v1/checks/publish-s3-kms.nf/.checks Normal file
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@@ -0,0 +1,30 @@
#!/bin/bash
BUCKET="nf-kms-xyz"
PREFIX="work/ci-test/publish-s3/$(uuidgen)"
OUTDIR="s3://$BUCKET/$PREFIX"
function check_kms_key() {
aws s3api head-object --bucket "$BUCKET" --key "$PREFIX/HELLO.tsv" | grep -c e5109f93-b42d-4c26-89ee-8b251029a41d
}
# Skip test if AWS keys are missing
if [ -z "$AWS_ACCESS_KEY_ID" ]; then
echo "Missing AWS credentials -- Skipping test"
exit 0
fi
#
# run normal mode
#
$NXF_RUN -c .config --outdir "$OUTDIR" | tee .stdout
[[ $(grep INFO .nextflow.log | grep -c 'Submitted process') == 1 ]] || false
[[ $(check_kms_key) == 1 ]] || false
#
# run resume mode
#
$NXF_RUN -c .config --outdir "$OUTDIR" -resume | tee .stdout
[[ $(grep INFO .nextflow.log | grep -c 'Cached process') == 1 ]] || false
[[ $(check_kms_key) == 1 ]] || false

2
nextflow/tests-v1/checks/publish-s3-kms.nf/.config Normal file
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@@ -0,0 +1,2 @@
aws.client.storageEncryption = 'aws:kms'
aws.client.storageKmsKeyId = 'arn:aws:kms:eu-west-1:195996028523:key/e5109f93-b42d-4c26-89ee-8b251029a41d'

24
nextflow/tests-v1/checks/publish-s3.nf/.checks Normal file
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@@ -0,0 +1,24 @@
function count_hello() {
rm -rf hello
aws s3 cp --only-show-errors s3://nextflow-ci/work/ci-test/publish-s3/HELLO.tsv hello && < hello grep 'Hello, world' -c
}
# Skip test if AWS keys are missing
if [ -z "$AWS_ACCESS_KEY_ID" ]; then
echo "Missing AWS credentials -- Skipping test"
exit 0
fi
#
# run normal mode
#
$NXF_RUN | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
#
# run resume mode
#
$NXF_RUN -resume | tee .stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 1 ]] || false

11
nextflow/tests-v1/checks/publish-saveas.nf/.checks Normal file
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@@ -0,0 +1,11 @@
echo First run
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 3 ]] || false
[[ -f results/alpha/file_1.txt ]] || false
[[ -f results/gamma/file_3.txt ]] || false
[[ ! -f results/file_2.txt ]] || false
[[ ! -f results/alpha/file_2.txt ]] || false
[[ ! -f results/gamma/file_2.txt ]] || false

7
nextflow/tests-v1/checks/qrun.sh Executable file
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@@ -0,0 +1,7 @@
#!/bin/bash
launch_cmd=../../launch.sh
export NXF_ANSI_LOG=false
export WITH_DOCKER=${WITH_DOCKER:=''}
export NXF_CMD=$(realpath $launch_cmd)
export TEST_JDK=17
bash run.sh "$1"

24
nextflow/tests-v1/checks/race.nf/.checks Normal file
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@@ -0,0 +1,24 @@
#
# run normal mode
#
$NXF_RUN
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > proc1'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > proc2'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > proc3'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > proc4'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > proc5'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > proc6'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > proc7'` == 3 ]] || false
$NXF_RUN
[[ `grep INFO .nextflow.log | grep -c '\[skipping\] Stored process > proc1'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c '\[skipping\] Stored process > proc2'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c '\[skipping\] Stored process > proc3'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c '\[skipping\] Stored process > proc4'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c '\[skipping\] Stored process > proc5'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c '\[skipping\] Stored process > proc6'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c '\[skipping\] Stored process > proc7'` == 3 ]] || false

58
nextflow/tests-v1/checks/repeaters.nf/.checks Normal file
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@@ -0,0 +1,58 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > hola'` == 12 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 2 ]] || false
grep 'x: 1; y: Ciao; z: alpha' stdout
grep 'x: 1; y: Ciao; z: beta' stdout
grep 'x: 1; y: Ciao; z: delta' stdout
grep 'x: 1; y: Hola; z: alpha' stdout
grep 'x: 1; y: Hola; z: beta' stdout
grep 'x: 1; y: Hola; z: delta' stdout
grep 'x: 2; y: Ciao; z: alpha' stdout
grep 'x: 2; y: Ciao; z: beta' stdout
grep 'x: 2; y: Ciao; z: delta' stdout
grep 'x: 2; y: Hola; z: alpha' stdout
grep 'x: 2; y: Hola; z: beta' stdout
grep 'x: 2; y: Hola; z: delta' stdout
grep -F 'foo [a, b]' stdout
grep -F 'foo [c, d]' stdout
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > hola'` == 12 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 2 ]] || false
grep 'x: 1; y: Ciao; z: alpha' stdout
grep 'x: 1; y: Ciao; z: beta' stdout
grep 'x: 1; y: Ciao; z: delta' stdout
grep 'x: 1; y: Hola; z: alpha' stdout
grep 'x: 1; y: Hola; z: beta' stdout
grep 'x: 1; y: Hola; z: delta' stdout
grep 'x: 2; y: Ciao; z: alpha' stdout
grep 'x: 2; y: Ciao; z: beta' stdout
grep 'x: 2; y: Ciao; z: delta' stdout
grep 'x: 2; y: Hola; z: alpha' stdout
grep 'x: 2; y: Hola; z: beta' stdout
grep 'x: 2; y: Hola; z: delta' stdout
grep -F 'foo [a, b]' stdout
grep -F 'foo [c, d]' stdout

18
nextflow/tests-v1/checks/resume-retried-task.nf/.checks Normal file
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@@ -0,0 +1,18 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 1 ]] || false
[[ `< .nextflow.log grep -c 'Re-submitted process > foo'` == 2 ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `< .nextflow.log grep -c 'Cached process > foo'` == 1 ]] || false

13
nextflow/tests-v1/checks/retry-ignore.nf/.checks Normal file
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@@ -0,0 +1,13 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 1 ]] || false
[[ `< .nextflow.log grep -c 'Re-submitted process > foo'` == 1 ]] || false
[[ `< .nextflow.log grep -c 'Error is ignored'` == 1 ]] || false

100
nextflow/tests-v1/checks/run.sh Executable file
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@@ -0,0 +1,100 @@
#!/bin/bash
set -u
trap "exit" INT
NORMAL=$(tput sgr0)
GREEN=$(tput setaf 2; tput bold)
YELLOW=$(tput setaf 3)
RED=$(tput setaf 1)
function echo_red() {
echo -e "$RED$*$NORMAL"
}
function echo_green() {
echo -e "$GREEN$*$NORMAL"
}
function echo_yellow() {
echo -e "$YELLOW$*$NORMAL"
}
#
# Some vars
#
NXF_CMD=${NXF_CMD:-nextflow}
NXF_SYNTAX_PARSER=v1
REPORT=$PWD/.report
WITH_DOCKER=${WITH_DOCKER:=''}
#
# Clean scratch dir
#
export NXF_WORK=$PWD/scratch
rm -rf $NXF_WORK
function run_checks() {
NXF_SCRIPT="../../$1"
NXF_RUN="$NXF_CMD -q run $NXF_SCRIPT"
export NXF_SCRIPT
export NXF_CMD
export NXF_RUN
set +e
if [ -f $1/.checks ]; then
cd $basename;
rm -rf *
bash -ex .checks &> checks.out
else
mkdir -p $1
cd $1
$NXF_RUN > checks.out
fi
ret=$?
set -e
if [[ $ret != 0 ]]; then
echo "~ Test '$1' run failed" >> $REPORT
# dump error output
[[ -s checks.out ]] && cat checks.out | sed 's/^/ /'>> $REPORT
echo '' >> $REPORT
# dump nextflow log file
[[ -f .nextflow.log ]] && cat .nextflow.log >> $REPORT
echo '' >> $REPORT
exit 1
fi
}
rm -rf $REPORT
list=${1:-'../*.nf'}
function can_run() {
if [[ $(grep -c "$1" .PARSER-V1) != 0 ]]; then
echo 'yes'
else
echo 'no'
fi
}
for x in $list; do
basename=$(basename $x)
if [[ $(can_run $basename) == 'yes' ]]; then
echo "> Running test: $basename"
( set -e;
run_checks $basename
)
else
echo "- Ignoring test: $basename"
fi
done
if [[ -s $REPORT ]]; then
echo -e "$RED"
cat $REPORT
echo -e "$NORMAL"
exit 1
fi

32
nextflow/tests-v1/checks/s3-files.nf/.checks Normal file
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@@ -0,0 +1,32 @@
set -e
export NXF_PLUGINS_DEFAULT=nf-amazon
# Skip test if AWS keys are missing
if [[ ! $AWS_ACCESS_KEY_ID ]]; then
echo "Skip s3-files test since AWS keys are not available"
exit 0
fi
#
# run normal mode
#
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > bar (gut)'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > bar (liver)'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > bar (lung)'` == 1 ]] || false
cmp stdout .expected || false
#
# run resume mode
#
$NXF_RUN -resume | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process > foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > bar (gut)'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > bar (liver)'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > bar (lung)'` == 1 ]] || false
cmp stdout .expected || false

10
nextflow/tests-v1/checks/s3-files.nf/.expected Normal file
View File

@@ -0,0 +1,10 @@
>1 dna:chromosome chromosome:Galgal4:1:48849500:49020500:1
TGAAGCTTATCGTGTACTCTGTCTTCAGAAGCACAAGGACAATTAACATTCAATAGCAAG
GTCCTGTATTTATTTGTCTGAATAAATAAATAAGCATAATATATAATAAATAAATACTAT
TCAGCCTCTCACCAATAACAATAGTACCCACGCACATATTGCATAATTACAAAACATCCT
GACAGATCTGTGTGGGTGATAGACCAGAAATACCAGCTCAAATTAACTCTACAAAGAACT
ATATCATGGAACTTAGTGAAAAGTGATTTTTGGTTCCTGATTCTATGGCGCTTTGTTCTG
ACCTCTGTTTCATTGGATAATAAACAACCAGACTAGATTAAACAGTGTGTATTTGAAACA
GAAAATCAGTATAGACTTCCTGATTGAAATCTATTCTCAATCTTCTGGAATGCTCAAAGA
TACTCAGGAATAGAAATTGGAAGAGCAAAAATATCGACAAATTTGTTCCATGAGCTCCCT
CAACCTTTGTAAGATTACTCTCTGTGCAGTAGTTTTCTAGTCCTTTTTCAGTGGTTGATG

18
nextflow/tests-v1/checks/s3-public/.checks Normal file
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@@ -0,0 +1,18 @@
set -e
# enable amazon plugin
export NXF_PLUGINS_DEFAULT=nf-amazon
# this test needs to validate the ability to access S3 public data
# in anonymous manner, therefore make sure to clear any aws credentials
unset AWS_ACCESS_KEY_ID
unset AWS_SECRET_ACCESS_KEY
unset AWS_SECRET_KEY
unset AWS_ACCESS_KEY
#
# run normal mode
#
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false

17
nextflow/tests-v1/checks/s3-report.nf/.checks Normal file
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@@ -0,0 +1,17 @@
set -e
export NXF_PLUGINS_DEFAULT=nf-amazon
# Skip test if AWS keys are missing
if [[ ! $AWS_ACCESS_KEY_ID ]]; then
echo "Skip s3-files test since AWS keys are not available"
exit 0
fi
#
# run normal mode
#
$NXF_CMD -trace com.upplication.s3fs run nextflow-io/hello \
-with-trace s3://nextflow-ci/test/trace.txt \
-with-report s3://nextflow-ci/test/report.html \
| tee stdout

37
nextflow/tests-v1/checks/shell-script.nf/.checks Normal file
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@@ -0,0 +1,37 @@
#
# run normal mode
#
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 2 ]] || false
< stdout grep "Home: $HOME - Input: alpha zzz" || false
< stdout grep "Home: $HOME - Input: omega zzz" || false
#
# run resume mode
#
$NXF_RUN -resume | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 2 ]] || false
< stdout grep "Home: $HOME - Input: alpha zzz" || false
< stdout grep "Home: $HOME - Input: omega zzz" || false
#
# run changing params does not hit cache
#
$NXF_RUN -resume --data xxx | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 2 ]] || false
< stdout grep "Home: $HOME - Input: alpha xxx" || false
< stdout grep "Home: $HOME - Input: omega xxx" || false
#
# now cache is ok
#
$NXF_RUN -resume --data xxx | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 2 ]] || false
< stdout grep "Home: $HOME - Input: alpha xxx" || false
< stdout grep "Home: $HOME - Input: omega xxx" || false

29
nextflow/tests-v1/checks/singleton.nf/.checks Normal file
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@@ -0,0 +1,29 @@
#
# run normal mode
#
echo ''
$NXF_RUN -process.debug | tee stdout
[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 1 ]] || false
[[ `< .nextflow.log grep -c 'Submitted process > bar (1)'` == 1 ]] || false
[[ `< .nextflow.log grep -c 'Submitted process > bar (2)'` == 1 ]] || false
[[ `< .nextflow.log grep -c 'Submitted process > bar (3)'` == 1 ]] || false
[[ `< stdout grep -c 'Hello1'` == 1 ]] || false
[[ `< stdout grep -c 'Hello2'` == 1 ]] || false
[[ `< stdout grep -c 'Hello3'` == 1 ]] || false
#
# RESUME mode
#
echo ''
$NXF_RUN -resume -process.debug | tee stdout
[[ `< .nextflow.log grep -c 'Cached process > foo'` == 1 ]] || false
[[ `< .nextflow.log grep -c 'Cached process > bar (1)'` == 1 ]] || false
[[ `< .nextflow.log grep -c 'Cached process > bar (2)'` == 1 ]] || false
[[ `< .nextflow.log grep -c 'Cached process > bar (3)'` == 1 ]] || false
[[ `< stdout grep -c 'Hello1'` == 1 ]] || false
[[ `< stdout grep -c 'Hello2'` == 1 ]] || false
[[ `< stdout grep -c 'Hello3'` == 1 ]] || false

26
nextflow/tests-v1/checks/splitLetters.nf/.checks Normal file
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@@ -0,0 +1,26 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > splitLetters'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > massage'` == 2 ]] || false
grep 'HELLO' stdout
grep 'WORLD!' stdout
#
# RESUME mode
#
echo ''
$NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > splitLetters'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > massage'` == 2 ]] || false
grep 'HELLO' stdout
grep 'WORLD!' stdout

23
nextflow/tests-v1/checks/stage-file.nf/.checks Normal file
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@@ -0,0 +1,23 @@
set -e
#
# run normal mode
#
echo ''
NXF_WRAPPER_STAGE_FILE_THRESHOLD='100' $NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 2 ]] || false
TASK_DIR=`$NXF_CMD log last -F "process == 'bar'"`
[[ `cat $TASK_DIR/.command.stage | wc -l` -eq 19 ]] || false
#
# RESUME mode
#
echo ''
NXF_WRAPPER_STAGE_FILE_THRESHOLD='100' $NXF_RUN -resume | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process'` == 2 ]] || false
TASK_DIR=`$NXF_CMD log last -F "process == 'bar'"`
[[ `cat $TASK_DIR/.command.stage | wc -l` -eq 19 ]] || false

39
nextflow/tests-v1/checks/storeCache.nf/.checks Normal file
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@@ -0,0 +1,39 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > storeCache'` == 3 ]] || false
grep 'cache/Ciao.txt' stdout
grep 'cache/Hola.txt' stdout
grep 'cache/Hello.txt' stdout
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Stored process > storeCache'` == 3 ]] || false
grep 'cache/Ciao.txt' stdout
grep 'cache/Hola.txt' stdout
grep 'cache/Hello.txt' stdout
#
# run resume mode
#
echo ''
$NXF_RUN -resume| tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Stored process > storeCache'` == 3 ]] || false
grep 'cache/Ciao.txt' stdout
grep 'cache/Hola.txt' stdout
grep 'cache/Hello.txt' stdout

11
nextflow/tests-v1/checks/stub-retry.nf/.checks Normal file
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@@ -0,0 +1,11 @@
set -e
echo ''
$NXF_RUN -stub | tee stdout
[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > stubtest'` == 1 ]] || false
[[ `grep 'INFO' .nextflow.log | grep -c 'Re-submitted process > stubtest'` == 1 ]] || false
[[ `grep -c 'Stubbing. Creating file' stdout` == 1 ]] || false

27
nextflow/tests-v1/checks/subdirs.nf/.checks Normal file
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@@ -0,0 +1,27 @@
set -e
#
# run normal mode
#
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
< stdout grep 'link_1.fasta'
< stdout grep 'link_2.fasta'
< stdout grep 'link_3.fasta'
< stdout grep 'alpha.txt'
< stdout grep 'beta.txt'
#
# run resume mode
#
$NXF_RUN -resume | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 1 ]] || false
< stdout grep 'link_1.fasta'
< stdout grep 'link_2.fasta'
< stdout grep 'link_3.fasta'
< stdout grep 'alpha.txt'
< stdout grep 'beta.txt'

19
nextflow/tests-v1/checks/subworkflow-take.nf/.checks Normal file
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@@ -0,0 +1,19 @@
set -e
rm * || true
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'process > flow1:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'process > flow1:bar'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'process > flow2:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'process > flow2:bar'` == 1 ]] || false
rm * || true
$NXF_RUN -resume | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process > flow1:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > flow1:bar'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > flow2:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > flow2:bar'` == 1 ]] || false

36
nextflow/tests-v1/checks/subworkflow.nf/.checks Normal file
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@@ -0,0 +1,36 @@
set -e
rm * || true
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'process > test1:flow1:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'process > test1:flow1:bar'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'process > test1:flow2:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'process > test1:flow2:baz'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'process > test2:flow1:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'process > test2:flow1:bar'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'process > test2:flow2:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'process > test2:flow2:baz'` == 1 ]] || false
[[ `<test1.txt grep -c 'HELLO'` == 1 ]]
[[ `<test1.txt grep -c 'olleH'` == 1 ]]
[[ `<test2.txt grep -c 'HELLO'` == 1 ]]
[[ `<test2.txt grep -c 'olleH'` == 1 ]]
rm * || true
$NXF_RUN -resume | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process > test1:flow1:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > test1:flow1:bar'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > test1:flow2:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > test1:flow2:baz'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > test2:flow1:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > test2:flow1:bar'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > test2:flow2:foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > test2:flow2:baz'` == 1 ]] || false
[[ `<test1.txt grep -c 'HELLO'` == 1 ]]
[[ `<test1.txt grep -c 'olleH'` == 1 ]]
[[ `<test2.txt grep -c 'HELLO'` == 1 ]]
[[ `<test2.txt grep -c 'olleH'` == 1 ]]

21
nextflow/tests-v1/checks/tag-resume.nf/.checks Normal file
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@@ -0,0 +1,21 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN -c ../../tag-resume.config | tee stdout
grep -c 'Submitted process > test (My Tool)' .nextflow.log
grep 'Hola' stdout
#
# run resume mode
#
echo ''
$NXF_RUN -c ../../tag-resume.config -resume| tee stdout
grep -c 'Cached process > test (My Tool)' .nextflow.log
grep 'Hola' stdout

34
nextflow/tests-v1/checks/tagging-lazy.nf/.checks Normal file
View File

@@ -0,0 +1,34 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
grep -c 'Submitted process > foo (alpha.fastq)' .nextflow.log
grep -c 'Submitted process > foo (delta.fastq)' .nextflow.log
grep -c 'Submitted process > foo (gamma.fastq)' .nextflow.log
grep -c 'Submitted process > foo (omega.fastq)' .nextflow.log
grep 'alpha' stdout
grep 'delta' stdout
grep 'gamma' stdout
grep 'omega' stdout
#
# run resume mode
#
echo ''
$NXF_RUN -resume| tee stdout
grep -c 'Cached process > foo (alpha.fastq)' .nextflow.log
grep -c 'Cached process > foo (delta.fastq)' .nextflow.log
grep -c 'Cached process > foo (gamma.fastq)' .nextflow.log
grep -c 'Cached process > foo (omega.fastq)' .nextflow.log
grep 'alpha' stdout
grep 'delta' stdout
grep 'gamma' stdout
grep 'omega' stdout

34
nextflow/tests-v1/checks/tagging.nf/.checks Normal file
View File

@@ -0,0 +1,34 @@
set -e
#
# run normal mode
#
echo ''
$NXF_RUN | tee stdout
grep -c 'Submitted process > foo (alpha)' .nextflow.log
grep -c 'Submitted process > foo (delta)' .nextflow.log
grep -c 'Submitted process > foo (gamma)' .nextflow.log
grep -c 'Submitted process > foo (omega)' .nextflow.log
grep 'alpha' stdout
grep 'delta' stdout
grep 'gamma' stdout
grep 'omega' stdout
#
# run resume mode
#
echo ''
$NXF_RUN -resume| tee stdout
grep -c 'Cached process > foo (alpha)' .nextflow.log
grep -c 'Cached process > foo (delta)' .nextflow.log
grep -c 'Cached process > foo (gamma)' .nextflow.log
grep -c 'Cached process > foo (omega)' .nextflow.log
grep 'alpha' stdout
grep 'delta' stdout
grep 'gamma' stdout
grep 'omega' stdout

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