Set process label to `process_single` for modules with no `task.cpus` usage (#2076)
* Set process label to `process_single` for modules with no `task.cpus` usage * Fix tests of 'borked' modules * prettier * More modules are single-threaded and can use process_single * Adding process_single to hmmer/esl* modules * Fix failing tests * Prettier Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>master
parent
46ad627a73
commit
90aef30f43
@ -1,110 +1,77 @@
|
||||
- name: damageprofiler
|
||||
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
|
||||
- name: damageprofiler test_damageprofiler
|
||||
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config -c ./tests/modules/damageprofiler/nextflow.config
|
||||
tags:
|
||||
- damageprofiler
|
||||
files:
|
||||
- path: output/damageprofiler/test/3p_freq_misincorporations.txt
|
||||
md5sum: de3b84d946a6b63cdcfadf82bf6854c0
|
||||
- path: output/damageprofiler/test/3pGtoA_freq.txt
|
||||
md5sum: 61c903b1504ed7d7182570dfc75e4498
|
||||
md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
|
||||
- path: output/damageprofiler/test/3p_freq_misincorporations.txt
|
||||
md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
|
||||
- path: output/damageprofiler/test/5pCtoT_freq.txt
|
||||
md5sum: 15a75b60ee519b61ce04a83fe3afe855
|
||||
md5sum: 38b5d7c87ec2d8422bc5587095711c5f
|
||||
- path: output/damageprofiler/test/5p_freq_misincorporations.txt
|
||||
md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
|
||||
- path: output/damageprofiler/test/DamagePlot_five_prime.svg
|
||||
md5sum: 05e041ff47e7c6d08ede51f5c81a2464
|
||||
- path: output/damageprofiler/test/DNA_comp_genome.txt
|
||||
md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
|
||||
- path: output/damageprofiler/test/DNA_composition_sample.txt
|
||||
md5sum: 16be9c91a06fa7defee376230b12862f
|
||||
- path: output/damageprofiler/test/DamagePlot.pdf
|
||||
- path: output/damageprofiler/test/DamagePlot_five_prime.svg
|
||||
- path: output/damageprofiler/test/DamagePlot_three_prime.svg
|
||||
- path: output/damageprofiler/test/DamageProfiler.log
|
||||
contains:
|
||||
- "FINISHED SUCCESSFULLY"
|
||||
- path: output/damageprofiler/test/Length_plot.pdf
|
||||
- path: output/damageprofiler/test/Length_plot_combined_data.svg
|
||||
- path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
|
||||
- path: output/damageprofiler/test/dmgprof.json
|
||||
md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
|
||||
- path: output/damageprofiler/test/DNA_comp_genome.txt
|
||||
md5sum: fea48af1ecf491b439d36d4a919473df
|
||||
- path: output/damageprofiler/test/DNA_composition_sample.txt
|
||||
md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
|
||||
md5sum: a011a47edaadb3a07527c329a6492570
|
||||
- path: output/damageprofiler/test/editDistance.txt
|
||||
md5sum: 7590dac007633ee11025cc99ec9f009b
|
||||
- path: output/damageprofiler/test/edit_distance.pdf
|
||||
- path: output/damageprofiler/test/edit_distance.svg
|
||||
- path: output/damageprofiler/test/editDistance.txt
|
||||
md5sum: 04d14b449a5afa8b5dbff0dfa762356b
|
||||
- path: output/damageprofiler/test/Length_plot_combined_data.svg
|
||||
- path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
|
||||
- path: output/damageprofiler/test/Length_plot.pdf
|
||||
- path: output/damageprofiler/test/lgdistribution.txt
|
||||
md5sum: df2e19195185ea9ee05e8e84b2948f36
|
||||
md5sum: 583fd98094de3fb462b133daeaadcf52
|
||||
- path: output/damageprofiler/test/misincorporation.txt
|
||||
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
|
||||
md5sum: 25119c0fcc8839fdbb3ed10922fb07f4
|
||||
|
||||
- name: damageprofiler_reference
|
||||
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
|
||||
- name: damageprofiler test_damageprofiler_reference
|
||||
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config -c ./tests/modules/damageprofiler/nextflow.config
|
||||
tags:
|
||||
- damageprofiler
|
||||
files:
|
||||
- path: output/damageprofiler/test/3p_freq_misincorporations.txt
|
||||
md5sum: de3b84d946a6b63cdcfadf82bf6854c0
|
||||
- path: output/damageprofiler/test/3pGtoA_freq.txt
|
||||
md5sum: 61c903b1504ed7d7182570dfc75e4498
|
||||
md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
|
||||
- path: output/damageprofiler/test/3p_freq_misincorporations.txt
|
||||
md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
|
||||
- path: output/damageprofiler/test/5pCtoT_freq.txt
|
||||
md5sum: 15a75b60ee519b61ce04a83fe3afe855
|
||||
md5sum: 38b5d7c87ec2d8422bc5587095711c5f
|
||||
- path: output/damageprofiler/test/5p_freq_misincorporations.txt
|
||||
md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
|
||||
- path: output/damageprofiler/test/DamagePlot_five_prime.svg
|
||||
md5sum: 05e041ff47e7c6d08ede51f5c81a2464
|
||||
- path: output/damageprofiler/test/DNA_comp_genome.txt
|
||||
md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
|
||||
- path: output/damageprofiler/test/DNA_composition_sample.txt
|
||||
md5sum: 16be9c91a06fa7defee376230b12862f
|
||||
- path: output/damageprofiler/test/DamagePlot.pdf
|
||||
- path: output/damageprofiler/test/DamagePlot_five_prime.svg
|
||||
- path: output/damageprofiler/test/DamagePlot_three_prime.svg
|
||||
- path: output/damageprofiler/test/DamageProfiler.log
|
||||
contains:
|
||||
- "FINISHED SUCCESSFULLY"
|
||||
- path: output/damageprofiler/test/Length_plot.pdf
|
||||
- path: output/damageprofiler/test/Length_plot_combined_data.svg
|
||||
- path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
|
||||
- path: output/damageprofiler/test/dmgprof.json
|
||||
md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
|
||||
- path: output/damageprofiler/test/DNA_comp_genome.txt
|
||||
md5sum: fea48af1ecf491b439d36d4a919473df
|
||||
- path: output/damageprofiler/test/DNA_composition_sample.txt
|
||||
md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
|
||||
md5sum: a011a47edaadb3a07527c329a6492570
|
||||
- path: output/damageprofiler/test/editDistance.txt
|
||||
md5sum: 7590dac007633ee11025cc99ec9f009b
|
||||
- path: output/damageprofiler/test/edit_distance.pdf
|
||||
- path: output/damageprofiler/test/edit_distance.svg
|
||||
- path: output/damageprofiler/test/editDistance.txt
|
||||
md5sum: 04d14b449a5afa8b5dbff0dfa762356b
|
||||
- path: output/damageprofiler/test/Length_plot_combined_data.svg
|
||||
- path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
|
||||
- path: output/damageprofiler/test/Length_plot.pdf
|
||||
- path: output/damageprofiler/test/lgdistribution.txt
|
||||
md5sum: df2e19195185ea9ee05e8e84b2948f36
|
||||
md5sum: 583fd98094de3fb462b133daeaadcf52
|
||||
- path: output/damageprofiler/test/misincorporation.txt
|
||||
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
|
||||
md5sum: 25119c0fcc8839fdbb3ed10922fb07f4
|
||||
|
||||
- name: damageprofiler_specieslist
|
||||
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
|
||||
- name: damageprofiler test_damageprofiler_specieslist
|
||||
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config -c ./tests/modules/damageprofiler/nextflow.config
|
||||
tags:
|
||||
- damageprofiler
|
||||
files:
|
||||
- path: output/damageprofiler/test/chr22/3p_freq_misincorporations.txt
|
||||
md5sum: de3b84d946a6b63cdcfadf82bf6854c0
|
||||
- path: output/damageprofiler/test/chr22/3pGtoA_freq.txt
|
||||
md5sum: 61c903b1504ed7d7182570dfc75e4498
|
||||
- path: output/damageprofiler/test/chr22/5pCtoT_freq.txt
|
||||
md5sum: 15a75b60ee519b61ce04a83fe3afe855
|
||||
- path: output/damageprofiler/test/chr22/5p_freq_misincorporations.txt
|
||||
md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
|
||||
- path: output/damageprofiler/test/chr22/DamagePlot_five_prime.svg
|
||||
- path: output/damageprofiler/test/chr22/DamagePlot.pdf
|
||||
- path: output/damageprofiler/test/chr22/DamagePlot_three_prime.svg
|
||||
- path: output/damageprofiler/test/DamageProfiler.log
|
||||
contains:
|
||||
- "FINISHED SUCCESSFULLY"
|
||||
- path: output/damageprofiler/test/chr22/dmgprof.json
|
||||
md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
|
||||
- path: output/damageprofiler/test/chr22/DNA_comp_genome.txt
|
||||
md5sum: fea48af1ecf491b439d36d4a919473df
|
||||
- path: output/damageprofiler/test/chr22/DNA_composition_sample.txt
|
||||
md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
|
||||
- path: output/damageprofiler/test/chr22/edit_distance.pdf
|
||||
- path: output/damageprofiler/test/chr22/edit_distance.svg
|
||||
- path: output/damageprofiler/test/chr22/editDistance.txt
|
||||
md5sum: 04d14b449a5afa8b5dbff0dfa762356b
|
||||
- path: output/damageprofiler/test/chr22/Length_plot_combined_data.svg
|
||||
- path: output/damageprofiler/test/chr22/Length_plot_forward_reverse_separated.svg
|
||||
- path: output/damageprofiler/test/chr22/Length_plot.pdf
|
||||
- path: output/damageprofiler/test/chr22/lgdistribution.txt
|
||||
md5sum: df2e19195185ea9ee05e8e84b2948f36
|
||||
- path: output/damageprofiler/test/chr22/misincorporation.txt
|
||||
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
|
||||
#contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
|
||||
|
@ -1,17 +1,17 @@
|
||||
- name: entrezdirect xtract test_entrezdirect_xtract_assembly
|
||||
command: nextflow run ./tests/modules/entrezdirect/xtract -entry test_entrezdirect_xtract_assembly -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/xtract/nextflow.config
|
||||
tags:
|
||||
- entrezdirect/xtract
|
||||
- entrezdirect
|
||||
- entrezdirect/xtract
|
||||
files:
|
||||
- path: output/entrezdirect/test_assembly.xml
|
||||
md5sum: 32f81147eea61df5814e87c2df1092a9
|
||||
- path: output/entrezdirect/test_assembly.txt
|
||||
md5sum: 17073db7c14890aef30f5e3f2d003d32
|
||||
|
||||
- name: entrezdirect xtract test_entrezdirect_xtract_genome
|
||||
command: nextflow run ./tests/modules/entrezdirect/xtract -entry test_entrezdirect_xtract_genome -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/xtract/nextflow.config
|
||||
tags:
|
||||
- entrezdirect/xtract
|
||||
- entrezdirect
|
||||
- entrezdirect/xtract
|
||||
files:
|
||||
- path: output/entrezdirect/test_genome.xml
|
||||
md5sum: af6242f231bdc147d6197edfd0954585
|
||||
- path: output/entrezdirect/test_genome.txt
|
||||
md5sum: 931279db7c80c5bb9ed523815898a9cd
|
||||
|
Loading…
Reference in New Issue