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nf-core_modules/tests/modules/fgbio/fastqtobam/test.yml

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Fgbio/fastqtobam (#1980) * fix samtools stats thread usage * fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums * Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads * Update busco to v5.4.3 and tar small files (#1970) * Update busco to v5.4.3 and tar small files * Fix file contain strings * Swap md5sums to contains for variable files * Simplify and generalize module * add test.yml * Update modules/fgbio/fastqtobam/meta.yml Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * add support + tests for cram output * more tweaks * update test.yml * prettier * try to fix tests * fix tests * prettier * drop checksum for cram Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-09-05 09:57:55 +00:00
- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_default
command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_default -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/fastqtobam/nextflow.config
Rewritten module fgbio/fastqtobam (#916) * added template for fastqtobam * porting old code into new template * update with missing getprocessname function * test completed - updating all * fixed linting issues * improved reading Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-10-27 17:06:06 +00:00
tags:
Fgbio/fastqtobam (#1980) * fix samtools stats thread usage * fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums * Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads * Update busco to v5.4.3 and tar small files (#1970) * Update busco to v5.4.3 and tar small files * Fix file contain strings * Swap md5sums to contains for variable files * Simplify and generalize module * add test.yml * Update modules/fgbio/fastqtobam/meta.yml Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * add support + tests for cram output * more tweaks * update test.yml * prettier * try to fix tests * fix tests * prettier * drop checksum for cram Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-09-05 09:57:55 +00:00
- fgbio
- fgbio/fastqtobam
files:
- path: output/fgbio/test.bam
md5sum: 83cd60e01e5ab90ea3729431ce401add
- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_cram
command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_cram -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/fastqtobam/nextflow.config
tags:
- fgbio
- fgbio/fastqtobam
files:
- path: output/fgbio/test.cram
- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_bam
command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/fastqtobam/nextflow.config
tags:
- fgbio
- fgbio/fastqtobam
files:
- path: output/fgbio/test.bam
md5sum: 83f879e3a302ca8a50dc9675be7a9216
- name: fgbio fastqtobam test_fgbio_fastqtobam_single
command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_single -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/fastqtobam/nextflow.config
tags:
- fgbio
Rewritten module fgbio/fastqtobam (#916) * added template for fastqtobam * porting old code into new template * update with missing getprocessname function * test completed - updating all * fixed linting issues * improved reading Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-10-27 17:06:06 +00:00
- fgbio/fastqtobam
Fgbio/fastqtobam (#1980) * fix samtools stats thread usage * fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums * Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads * Update busco to v5.4.3 and tar small files (#1970) * Update busco to v5.4.3 and tar small files * Fix file contain strings * Swap md5sums to contains for variable files * Simplify and generalize module * add test.yml * Update modules/fgbio/fastqtobam/meta.yml Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * add support + tests for cram output * more tweaks * update test.yml * prettier * try to fix tests * fix tests * prettier * drop checksum for cram Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-09-05 09:57:55 +00:00
files:
- path: output/fgbio/test.bam
md5sum: c08fe1b035b972808f05128e37e8e669
- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_umi
command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_umi -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/fastqtobam/nextflow.config
tags:
Rewritten module fgbio/fastqtobam (#916) * added template for fastqtobam * porting old code into new template * update with missing getprocessname function * test completed - updating all * fixed linting issues * improved reading Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-10-27 17:06:06 +00:00
- fgbio
Fgbio/fastqtobam (#1980) * fix samtools stats thread usage * fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums * Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads * Update busco to v5.4.3 and tar small files (#1970) * Update busco to v5.4.3 and tar small files * Fix file contain strings * Swap md5sums to contains for variable files * Simplify and generalize module * add test.yml * Update modules/fgbio/fastqtobam/meta.yml Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * add support + tests for cram output * more tweaks * update test.yml * prettier * try to fix tests * fix tests * prettier * drop checksum for cram Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-09-05 09:57:55 +00:00
- fgbio/fastqtobam
Rewritten module fgbio/fastqtobam (#916) * added template for fastqtobam * porting old code into new template * update with missing getprocessname function * test completed - updating all * fixed linting issues * improved reading Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-10-27 17:06:06 +00:00
files:
Fgbio/fastqtobam (#1980) * fix samtools stats thread usage * fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums * Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads * Update busco to v5.4.3 and tar small files (#1970) * Update busco to v5.4.3 and tar small files * Fix file contain strings * Swap md5sums to contains for variable files * Simplify and generalize module * add test.yml * Update modules/fgbio/fastqtobam/meta.yml Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * add support + tests for cram output * more tweaks * update test.yml * prettier * try to fix tests * fix tests * prettier * drop checksum for cram Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-09-05 09:57:55 +00:00
- path: output/fgbio/test.bam
Rewritten module fgbio/fastqtobam (#916) * added template for fastqtobam * porting old code into new template * update with missing getprocessname function * test completed - updating all * fixed linting issues * improved reading Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-10-27 17:06:06 +00:00
md5sum: 9510735554e5eff29244077a72075fb6
Fgbio/fastqtobam (#1980) * fix samtools stats thread usage * fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums * Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads * Update busco to v5.4.3 and tar small files (#1970) * Update busco to v5.4.3 and tar small files * Fix file contain strings * Swap md5sums to contains for variable files * Simplify and generalize module * add test.yml * Update modules/fgbio/fastqtobam/meta.yml Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * add support + tests for cram output * more tweaks * update test.yml * prettier * try to fix tests * fix tests * prettier * drop checksum for cram Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-09-05 09:57:55 +00:00
- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_custom_samplename
command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_custom_samplename -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/fastqtobam/nextflow.config
tags:
- fgbio
- fgbio/fastqtobam
files:
- path: output/fgbio/test.bam
md5sum: ab8d7d2d9c1559b19a501d120296ebe0
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