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nf-core_modules/tests/modules/star/align/test.yml

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Updated the version of STAR in align and genomegenerate modules (#604) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 12:30:52 +00:00
- name: star align test_star_alignment_single_end
command: nextflow run tests/modules/star/align -entry test_star_alignment_single_end -c tests/config/nextflow.config
Restructure tests to run individually for each module
2021-02-03 16:02:58 +00:00
tags:
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
- star/align
Added PL tag in read group information for downstream analysis (#649) Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-08-04 09:16:51 +00:00
- star
Restructure tests to run individually for each module
2021-02-03 16:02:58 +00:00
files:
Updated the version of STAR in align and genomegenerate modules (#604) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 12:30:52 +00:00
- path: output/index/star/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- path: output/index/star/Log.out
- path: output/index/star/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- path: output/index/star/SAindex
md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
- path: output/index/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- path: output/index/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- path: output/index/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- path: output/index/star/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- path: output/index/star/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- path: output/index/star/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- path: output/index/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- path: output/index/star/genomeParameters.txt
md5sum: 3097677f4d8b2cb66770b9e55d343a7f
- path: output/index/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- path: output/index/star/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- path: output/index/star/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- path: output/index/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
Restructure tests to run individually for each module
2021-02-03 16:02:58 +00:00
- path: output/star/test.Aligned.out.bam
Added PL tag in read group information for downstream analysis (#649) Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-08-04 09:16:51 +00:00
md5sum: b9f5e2f6a624b64c300fe25dc3ac801f
Updated the version of STAR in align and genomegenerate modules (#604) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 12:30:52 +00:00
- path: output/star/test.Log.final.out
- path: output/star/test.Log.out
- path: output/star/test.Log.progress.out
Restructure tests to run individually for each module
2021-02-03 16:02:58 +00:00
- path: output/star/test.SJ.out.tab
Updated the version of STAR in align and genomegenerate modules (#604) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 12:30:52 +00:00
- name: star align test_star_alignment_paired_end
command: nextflow run tests/modules/star/align -entry test_star_alignment_paired_end -c tests/config/nextflow.config
Restructure tests to run individually for each module
2021-02-03 16:02:58 +00:00
tags:
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
- star/align
Added PL tag in read group information for downstream analysis (#649) Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-08-04 09:16:51 +00:00
- star
Restructure tests to run individually for each module
2021-02-03 16:02:58 +00:00
files:
Updated the version of STAR in align and genomegenerate modules (#604) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 12:30:52 +00:00
- path: output/index/star/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- path: output/index/star/Log.out
- path: output/index/star/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- path: output/index/star/SAindex
md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
- path: output/index/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- path: output/index/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- path: output/index/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- path: output/index/star/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- path: output/index/star/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- path: output/index/star/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- path: output/index/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- path: output/index/star/genomeParameters.txt
md5sum: 3097677f4d8b2cb66770b9e55d343a7f
- path: output/index/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- path: output/index/star/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- path: output/index/star/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- path: output/index/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
Restructure tests to run individually for each module
2021-02-03 16:02:58 +00:00
- path: output/star/test.Aligned.out.bam
Added PL tag in read group information for downstream analysis (#649) Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-08-04 09:16:51 +00:00
md5sum: 38d08f0b944a2a1b981a250d675aa0d9
Update checksum modules using human GTF (#900) * update test yml star align * update test yml stringtie merge * update star genomegenerate yml * update test yml rsem calculateexpression Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-26 22:09:04 +00:00
- path: output/star/test.Log.final.out
Updated the version of STAR in align and genomegenerate modules (#604) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 12:30:52 +00:00
- path: output/star/test.Log.out
- path: output/star/test.Log.progress.out
Restructure tests to run individually for each module
2021-02-03 16:02:58 +00:00
- path: output/star/test.SJ.out.tab
Updated the version of STAR in align and genomegenerate modules (#604) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 12:30:52 +00:00
- name: star align test_star_alignment_paired_end_for_fusion
command: nextflow run tests/modules/star/align -entry test_star_alignment_paired_end_for_fusion -c tests/config/nextflow.config
tags:
- star/align
Added PL tag in read group information for downstream analysis (#649) Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-08-04 09:16:51 +00:00
- star
Updated the version of STAR in align and genomegenerate modules (#604) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 12:30:52 +00:00
files:
- path: output/index/star/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- path: output/index/star/Log.out
- path: output/index/star/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- path: output/index/star/SAindex
md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
- path: output/index/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- path: output/index/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- path: output/index/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- path: output/index/star/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- path: output/index/star/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- path: output/index/star/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- path: output/index/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- path: output/index/star/genomeParameters.txt
md5sum: 3097677f4d8b2cb66770b9e55d343a7f
- path: output/index/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- path: output/index/star/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- path: output/index/star/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- path: output/index/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam
Added PL tag in read group information for downstream analysis (#649) Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-08-04 09:16:51 +00:00
md5sum: c740d5177067c1fcc48ab7a16cd639d7
Updated the version of STAR in align and genomegenerate modules (#604) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 12:30:52 +00:00
- path: output/star/test.Log.final.out
- path: output/star/test.Log.out
- path: output/star/test.Log.progress.out
- path: output/star/test.SJ.out.tab
Added an optional output junction channel in STAR (#621) * Added an optional output channel for chimeric junctions * Fix in test.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-26 17:03:30 +00:00
- name: star align test_star_alignment_paired_end_for_starfusion
command: nextflow run tests/modules/star/align -entry test_star_alignment_paired_end_for_starfusion -c tests/config/nextflow.config
tags:
- star/align
Added PL tag in read group information for downstream analysis (#649) Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-08-04 09:16:51 +00:00
- star
Added an optional output junction channel in STAR (#621) * Added an optional output channel for chimeric junctions * Fix in test.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-26 17:03:30 +00:00
files:
- path: output/index/star/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- path: output/index/star/Log.out
- path: output/index/star/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- path: output/index/star/SAindex
md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
- path: output/index/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- path: output/index/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- path: output/index/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- path: output/index/star/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- path: output/index/star/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- path: output/index/star/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- path: output/index/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- path: output/index/star/genomeParameters.txt
md5sum: 3097677f4d8b2cb66770b9e55d343a7f
- path: output/index/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- path: output/index/star/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- path: output/index/star/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- path: output/index/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam
md5sum: a1bd1b40950a58ea2776908076160052
- path: output/star/test.Chimeric.out.junction
md5sum: 327629eb54032212f29e1c32cbac6975
- path: output/star/test.Log.final.out
- path: output/star/test.Log.out
- path: output/star/test.Log.progress.out
- path: output/star/test.SJ.out.tab
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