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Sfitz by readgroup and add FastQC #62
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d0d3a7b
process by readgroup in progress
sorelfitzgibbon adb0591
standardize algorithms to algorithm
sorelfitzgibbon ad00e21
samtools stats by readgroup
sorelfitzgibbon 046ce02
update changelog
sorelfitzgibbon 07b5458
fix mislabel
sorelfitzgibbon eb422cc
revert unintentional resource changes
sorelfitzgibbon ae43ccd
add fastqc
sorelfitzgibbon 68cf4b4
add fastqc module
sorelfitzgibbon b738e51
use process_afterscript
sorelfitzgibbon 27f1581
update changelog
sorelfitzgibbon 1c922f9
update nftest for fastqc
sorelfitzgibbon dff3a7a
fix nftest path
sorelfitzgibbon dbf3a01
merge with sfitz-by-readgroup complete and tested
sorelfitzgibbon 9fd01e9
use fastqc docker with samtools
sorelfitzgibbon c5407f8
fastqc by readgroup
sorelfitzgibbon 8653bbc
nftest paths updated
sorelfitzgibbon 20085c3
refactor channels
sorelfitzgibbon b34451e
add hg003 to NFTest
sorelfitzgibbon d049c14
update samtools
sorelfitzgibbon 53632de
pull main - samtools update
sorelfitzgibbon 19b68a2
use fastqc docker with samtools
sorelfitzgibbon 0e2c3df
add fastqc resource allocations
sorelfitzgibbon f95d47e
add fastqc threading and adjust resources
sorelfitzgibbon da059b8
add fastqc
sorelfitzgibbon 8f92e36
add fastqc to metadata.yaml
sorelfitzgibbon cc38b86
Bump the pipeline-submodules group with 2 updates
dependabot[bot] 9c9e207
Merge branch 'main' into sfitz-by-readgroup
sorelfitzgibbon 198b40c
add final newline
sorelfitzgibbon 91bf337
update readme
sorelfitzgibbon 4e2b724
update nftest.yml
sorelfitzgibbon 01b50bf
parameterize fastqc and add max gps to stats
sorelfitzgibbon e61b1ac
sanitize library ID
sorelfitzgibbon e6d0200
update test configs
sorelfitzgibbon 91f47d3
change process input variable names
sorelfitzgibbon a2f0489
add slurm logs and extra test files to .gitignore
sorelfitzgibbon fae512d
update readme
sorelfitzgibbon ecf44dd
update comments
sorelfitzgibbon 206c7e9
adjust run level triggers
sorelfitzgibbon 8587520
adjust log filename
sorelfitzgibbon 137874f
update nftests
sorelfitzgibbon 6ad240e
fix test name
sorelfitzgibbon 86cc4b2
remove out of date comments
sorelfitzgibbon 8fd7119
change process names
sorelfitzgibbon 9bb4d2f
rename bamqc_outformat to bamqc_output_format
sorelfitzgibbon 2a63bb4
rename bamqc_outformat to bamqc_output_format
sorelfitzgibbon 4e1e2fd
remove fastqc as default
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Original file line number | Diff line number | Diff line change |
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@@ -80,3 +80,8 @@ work/ | |
*.gz | ||
*.tar | ||
*.zip | ||
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# Other | ||
test/* | ||
test/*/* | ||
slurm-*.out |
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(question|standardization : non-blocking) Does this follow our NF standards?
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I believe so. The standards say:
"It’s ok to add an additional attribute if a process needs to be run more than once"
run_stats_SAMtools
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Right. I think placing the tool name as the last attribute would make more sense though (e.g. run_VariantRecalibratorSNP_GATK and run_VariantRecalibratorINDEL_GATK)? I'll defer this to Nextflow WG.
https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3193890/Nextflow+pipeline+standardization
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Oh I see! What are your thoughts on whether the three sections should be maintained?
run_statsReadgroups_SAMtools
vsrun_stats_readgroups_SAMtools
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I'm ok with maintaining the three sections and using
run_statsReadgroups_SAMtools