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nf-core_modules/tests/modules/umitools/dedup/test.yml

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Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
- name: umitools dedup test_umitools_dedup_no_umi
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_no_umi -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
tags:
- umitools/dedup
- umitools
files:
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
- path: output/umitools/test.dedup.bam
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
md5sum: 53b4edc399db81b87d2343e78af73cf0
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
- name: umitools dedup test_umitools_dedup_single_end_no_stats
command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_single_end_no_stats -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
tags:
- umitools/dedup
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
- umitools
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
files:
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
- path: output/bwa/bwa/genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: output/bwa/bwa/genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567
- path: output/bwa/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da
- path: output/bwa/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: output/bwa/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
- path: output/bwa/test.bam
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
md5sum: 3ecbe569cadb9b6c881917ce60779f75
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
- path: output/samtools/test.bam.bai
md5sum: 095af0ad3921212597ffd7c342ecd5a0
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
- path: output/umitools/test.dedup.bam
md5sum: 8f7c519e110d6515d858eda6b16727ac
- path: output/umitools/test.umi_extract.fastq.gz
- path: output/umitools/test.umi_extract.log
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
- name: umitools dedup test_umitools_dedup_paired_end_no_stats
command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end_no_stats -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
tags:
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
- umitools/dedup
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
- umitools
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
files:
- path: output/bwa/bwa/genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: output/bwa/bwa/genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567
- path: output/bwa/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da
- path: output/bwa/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: output/bwa/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1
- path: output/bwa/test.bam
md5sum: e7dcbac1825bf210409b762dbb4fec8f
- path: output/samtools/test.bam.bai
md5sum: f75780d1de7860329b7fb4afeadc4bed
- path: output/umitools/test.dedup.bam
md5sum: d75284de88b05569a66667e5b9936be9
- path: output/umitools/test.umi_extract.log
- path: output/umitools/test.umi_extract_1.fastq.gz
- path: output/umitools/test.umi_extract_2.fastq.gz
- name: umitools dedup test_umitools_dedup_paired_end_stats
command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end_stats -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config
tags:
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
- umitools/dedup
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
- umitools
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
files:
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
- path: output/bwa/bwa/genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: output/bwa/bwa/genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567
- path: output/bwa/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da
- path: output/bwa/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: output/bwa/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
- path: output/bwa/test.bam
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
md5sum: e7dcbac1825bf210409b762dbb4fec8f
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
- path: output/samtools/test.bam.bai
Update umitools/dedup module to make --output-stats optional
2022-05-23 21:31:09 +00:00
md5sum: f75780d1de7860329b7fb4afeadc4bed
- path: output/umitools/test.dedup.bam
md5sum: d75284de88b05569a66667e5b9936be9
- path: output/umitools/test.dedup_edit_distance.tsv
md5sum: c247a49b58768e6e2e86a6c08483e612
- path: output/umitools/test.dedup_per_umi.tsv
md5sum: 10e35ca37f2bfb521ac6dd7314951a68
- path: output/umitools/test.dedup_per_umi_per_position.tsv
md5sum: 2e1a12e6f720510880068deddeefe063
- path: output/umitools/test.umi_extract.log
- path: output/umitools/test.umi_extract_1.fastq.gz
- path: output/umitools/test.umi_extract_2.fastq.gz
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