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Fix read indexing in AdapterRemoval module (#1051)

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* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pydamage/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* answer PR comments and switch to bgzip

* fix read index

* update test.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
This commit is contained in:
Maxime Borry 2021-11-10 13:21:12 +01:00 committed by GitHub
parent 8b4bfb12bb
commit 24707f2144
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2 changed files with 8 additions and 8 deletions
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4
modules/adapterremoval/main.nf
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@ -49,7 +49,7 @@ process ADAPTERREMOVAL {
""" """
AdapterRemoval \\ AdapterRemoval \\
--file1 ${reads[0]} \\ --file1 ${reads[0]} \\
--file2 ${reads[0]} \\ --file2 ${reads[1]} \\
$options.args \\ $options.args \\
--basename $prefix \\ --basename $prefix \\
--threads $task.cpus \\ --threads $task.cpus \\
@ -68,7 +68,7 @@ process ADAPTERREMOVAL {
""" """
AdapterRemoval \\ AdapterRemoval \\
--file1 ${reads[0]} \\ --file1 ${reads[0]} \\
--file2 ${reads[0]} \\ --file2 ${reads[1]} \\
--collapse \\ --collapse \\
$options.args \\ $options.args \\
--basename $prefix \\ --basename $prefix \\

12
tests/modules/adapterremoval/test.yml
View file

@ -13,12 +13,12 @@
tags: tags:
- adapterremoval - adapterremoval
files: files:
- path: output/adapterremoval/test.pair2.trimmed.fastq.gz
md5sum: f076a9f666235e01a3281f8c46c9d010
- path: output/adapterremoval/test.log - path: output/adapterremoval/test.log
md5sum: bea86105aff4d27fe29c83e24498fefa md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
- path: output/adapterremoval/test.pair1.trimmed.fastq.gz - path: output/adapterremoval/test.pair1.trimmed.fastq.gz
md5sum: f076a9f666235e01a3281f8c46c9d010 md5sum: 294a6277f0139bd597e57c6fa31f39c7
- path: output/adapterremoval/test.pair2.trimmed.fastq.gz
md5sum: de7b38e2c881bced8671acb1ab452d78
- name: adapterremoval test_adapterremoval_paired_end_collapse - name: adapterremoval test_adapterremoval_paired_end_collapse
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
@ -26,6 +26,6 @@
- adapterremoval - adapterremoval
files: files:
- path: output/adapterremoval/test.log - path: output/adapterremoval/test.log
md5sum: 97cb97b3d03123ac88430768b2e36c59 md5sum: 7f0b2328152226e46101a535cce718b3
- path: output/adapterremoval/test.merged.fastq.gz - path: output/adapterremoval/test.merged.fastq.gz
md5sum: 50a4f9fdac6a24e211eb4dcf9f292bef md5sum: 07a8f725bfd3ecbeabdc41b32d898dee