nf-core_modules/tests/modules/samtools/view/test.yml

- name: samtools view test_samtools_view
  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
  tags:
    - samtools/view
    - samtools
  files:
    - path: output/samtools/test.bam
      md5sum: e6a9285be7b1c616dc4e17679fce5f1e

- name: samtools view test_samtools_view_cram
  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_cram -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
  tags:
    - samtools/view
    - samtools
  files:
    - path: output/samtools/test.cram

- name: samtools view test_samtools_view_convert
  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_convert -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
  tags:
    - samtools/view
    - samtools
  files:
    - path: output/samtools/test.bam
      md5sum: 4f4a97da17db79c78b1912da3cdc1d8f

- name: samtools view test_samtools_view_index
  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_index -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
  tags:
    - samtools/view
    - samtools
  files:
    - path: output/samtools/test.bam
      md5sum: b2d2482cea94adfc9628473792b0d215
    - path: output/samtools/test.bam.csi
      md5sum: 343a2085b436cab2123147dafd255607

- name: samtools view test_samtools_view_filter
  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_filter -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
  tags:
    - samtools/view
    - samtools
  files:
    - path: output/samtools/test.bam
      md5sum: d8e20876423cb1123a559e4347115249
    - path: output/samtools/test.bam.csi
      md5sum: b1d688576e59529271333aa50b3ad3ae

- name: samtools view test_samtools_view_stubs
  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_stubs -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
  tags:
    - samtools/view
    - samtools
  files:
    - path: output/samtools/test.bam
      md5sum: e6a9285be7b1c616dc4e17679fce5f1e
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> 2021-10-29 11:01:05 +00:00			`- name: samtools view test_samtools_view`
Update samtools view (#2096) * samtools view update * remove csi output * prettier * update meta 2022-09-23 12:03:59 +00:00			`command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config`
Restructure tests to run individually for each module 2021-02-03 16:02:58 +00:00			`tags:`
Update samtools view (#2096) * samtools view update * remove csi output * prettier * update meta 2022-09-23 12:03:59 +00:00			`- samtools/view`
add qname feature to samtools/view (#2115) * add qname feature to samtools_view * update tests * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * added filter tests Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> 2022-09-28 12:04:41 +00:00			`- samtools`
Restructure tests to run individually for each module 2021-02-03 16:02:58 +00:00			`files:`
Update samtools modules with config logic (#381) * fixing paths for test * fixing paths for test * fixing pats to tests * fixing paths to tests * fixing paths to tests * fixing paths for tests * fixing paths for tests * fixing paths for tests * fixing paths fro tests * fixing paths for tests * indentation fixes * typo * renaming test results according to new file name * replacing the md5sums * fixing brackets * replacing md5sums * fixing md5sums * fixing md5sums' * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml Co-authored-by: Ramon Rivera <ramon.rivera10@upr.edu> Co-authored-by: Ramon Rivera <riveravicens@gmail.com> 2021-03-24 18:15:30 +00:00			`- path: output/samtools/test.bam`
Update samtools view (#2098) * samtools view update * remove csi output * prettier * update meta * add index functionality * prettier * fixed test checks 2022-09-23 14:52:01 +00:00			`md5sum: e6a9285be7b1c616dc4e17679fce5f1e`
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> 2021-10-29 11:01:05 +00:00
			`- name: samtools view test_samtools_view_cram`
Update samtools view (#2096) * samtools view update * remove csi output * prettier * update meta 2022-09-23 12:03:59 +00:00			`command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config`
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> 2021-10-29 11:01:05 +00:00			`tags:`
Update samtools view (#2096) * samtools view update * remove csi output * prettier * update meta 2022-09-23 12:03:59 +00:00			`- samtools/view`
add qname feature to samtools/view (#2115) * add qname feature to samtools_view * update tests * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * added filter tests Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> 2022-09-28 12:04:41 +00:00			`- samtools`
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> 2021-10-29 11:01:05 +00:00			`files:`
			`- path: output/samtools/test.cram`
feat added tests for stubs 2022-05-02 09:59:08 +00:00
Update samtools view (#2096) * samtools view update * remove csi output * prettier * update meta 2022-09-23 12:03:59 +00:00			`- name: samtools view test_samtools_view_convert`
			`command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_convert -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config`
feat added tests for stubs 2022-05-02 09:59:08 +00:00			`tags:`
			`- samtools/view`
add qname feature to samtools/view (#2115) * add qname feature to samtools_view * update tests * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * added filter tests Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> 2022-09-28 12:04:41 +00:00			`- samtools`
Update samtools view (#2096) * samtools view update * remove csi output * prettier * update meta 2022-09-23 12:03:59 +00:00			`files:`
			`- path: output/samtools/test.bam`
Update samtools view (#2098) * samtools view update * remove csi output * prettier * update meta * add index functionality * prettier * fixed test checks 2022-09-23 14:52:01 +00:00			`md5sum: 4f4a97da17db79c78b1912da3cdc1d8f`

			`- name: samtools view test_samtools_view_index`
			`command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_index -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config`
			`tags:`
			`- samtools/view`
add qname feature to samtools/view (#2115) * add qname feature to samtools_view * update tests * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * added filter tests Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> 2022-09-28 12:04:41 +00:00			`- samtools`
Update samtools view (#2098) * samtools view update * remove csi output * prettier * update meta * add index functionality * prettier * fixed test checks 2022-09-23 14:52:01 +00:00			`files:`
			`- path: output/samtools/test.bam`
			`md5sum: b2d2482cea94adfc9628473792b0d215`
			`- path: output/samtools/test.bam.csi`
			`md5sum: 343a2085b436cab2123147dafd255607`
Update samtools view (#2096) * samtools view update * remove csi output * prettier * update meta 2022-09-23 12:03:59 +00:00
add qname feature to samtools/view (#2115) * add qname feature to samtools_view * update tests * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * added filter tests Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> 2022-09-28 12:04:41 +00:00			`- name: samtools view test_samtools_view_filter`
			`command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_filter -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config`
			`tags:`
			`- samtools/view`
			`- samtools`
			`files:`
			`- path: output/samtools/test.bam`
			`md5sum: d8e20876423cb1123a559e4347115249`
			`- path: output/samtools/test.bam.csi`
			`md5sum: b1d688576e59529271333aa50b3ad3ae`

Update samtools view (#2096) * samtools view update * remove csi output * prettier * update meta 2022-09-23 12:03:59 +00:00			`- name: samtools view test_samtools_view_stubs`
			`command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_stubs -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config`
			`tags:`
			`- samtools/view`
add qname feature to samtools/view (#2115) * add qname feature to samtools_view * update tests * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * added filter tests Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> 2022-09-28 12:04:41 +00:00			`- samtools`
feat added tests for stubs 2022-05-02 09:59:08 +00:00			`files:`
			`- path: output/samtools/test.bam`
Update samtools view (#2098) * samtools view update * remove csi output * prettier * update meta * add index functionality * prettier * fixed test checks 2022-09-23 14:52:01 +00:00			`md5sum: e6a9285be7b1c616dc4e17679fce5f1e`