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Add Bacillus fragilis alignments to test_data.config (#1054)

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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

* add bacillus fragilis alignments

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>
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Maxime Borry 2021-11-10 17:40:07 +01:00 committed by GitHub
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commit 56d5eb9834
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6
tests/config/test_data.config
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@ -267,6 +267,12 @@ params {
test1_2_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz"
test2_1_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz"
test2_2_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz"
test1_paired_end_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test1.bam"
test1_paired_end_sorted_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test1.sorted.bam"
test1_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai"
test2_paired_end_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test2.bam"
test2_paired_end_sorted_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test2.sorted.bam"
test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai"
}
'nanopore' {
test_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/nanopore/fastq/test.fastq.gz"