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nf-core_modules/tests/modules/adapterremoval/test.yml

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new module: AdapterRemoval (#309) * add adapterremoval module * fix indentations * switch to process_medium * update docker tests * remove duplicated entry * fix line ending * Update software/adapterremoval/main.nf * Update software/adapterremoval/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
- name: adapterremoval test_adapterremoval_single_end
Fix: removes hardcoded flags and 'custom' file output for AdapterRemoval (#1357) * fix: remove left-over unnecessary code * Removes hardcoded flags and more explicit output * Fix test md5
2022-03-03 09:01:39 +00:00
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
new module: AdapterRemoval (#309) * add adapterremoval module * fix indentations * switch to process_medium * update docker tests * remove duplicated entry * fix line ending * Update software/adapterremoval/main.nf * Update software/adapterremoval/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
tags:
- adapterremoval
files:
Refactor adapterremoval (#1491) * refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings
2022-04-04 19:40:35 +00:00
- path: output/adapterremoval/test.discarded.fastq.gz
- path: output/adapterremoval/test.settings
new module: AdapterRemoval (#309) * add adapterremoval module * fix indentations * switch to process_medium * update docker tests * remove duplicated entry * fix line ending * Update software/adapterremoval/main.nf * Update software/adapterremoval/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
md5sum: 2fd3d5d703b63ba33a83021fccf25f77
Refactor adapterremoval (#1491) * refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings
2022-04-04 19:40:35 +00:00
- path: output/adapterremoval/test.truncated.fastq.gz
new module: AdapterRemoval (#309) * add adapterremoval module * fix indentations * switch to process_medium * update docker tests * remove duplicated entry * fix line ending * Update software/adapterremoval/main.nf * Update software/adapterremoval/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
md5sum: 62139afee94defad5b83bdd0b8475a1f
Fix: removes hardcoded flags and 'custom' file output for AdapterRemoval (#1357) * fix: remove left-over unnecessary code * Removes hardcoded flags and more explicit output * Fix test md5
2022-03-03 09:01:39 +00:00
- path: output/adapterremoval/versions.yml
md5sum: ac5b46719719b7ee62739530b80869fc
new module: AdapterRemoval (#309) * add adapterremoval module * fix indentations * switch to process_medium * update docker tests * remove duplicated entry * fix line ending * Update software/adapterremoval/main.nf * Update software/adapterremoval/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
- name: adapterremoval test_adapterremoval_paired_end
Fix: removes hardcoded flags and 'custom' file output for AdapterRemoval (#1357) * fix: remove left-over unnecessary code * Removes hardcoded flags and more explicit output * Fix test md5
2022-03-03 09:01:39 +00:00
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
new module: AdapterRemoval (#309) * add adapterremoval module * fix indentations * switch to process_medium * update docker tests * remove duplicated entry * fix line ending * Update software/adapterremoval/main.nf * Update software/adapterremoval/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
tags:
- adapterremoval
files:
Refactor adapterremoval (#1491) * refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings
2022-04-04 19:40:35 +00:00
- path: output/adapterremoval/test.discarded.fastq.gz
- path: output/adapterremoval/test.settings
Fix read indexing in AdapterRemoval module (#1051) * 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 * fix read index * update test.yml 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>
2021-11-10 12:21:12 +00:00
md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
Refactor adapterremoval (#1491) * refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings
2022-04-04 19:40:35 +00:00
- path: output/adapterremoval/test.pair1.truncated.fastq.gz
Fix read indexing in AdapterRemoval module (#1051) * 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 * fix read index * update test.yml 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>
2021-11-10 12:21:12 +00:00
md5sum: 294a6277f0139bd597e57c6fa31f39c7
Refactor adapterremoval (#1491) * refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings
2022-04-04 19:40:35 +00:00
- path: output/adapterremoval/test.pair2.truncated.fastq.gz
Fix read indexing in AdapterRemoval module (#1051) * 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 * fix read index * update test.yml 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>
2021-11-10 12:21:12 +00:00
md5sum: de7b38e2c881bced8671acb1ab452d78
Fix: removes hardcoded flags and 'custom' file output for AdapterRemoval (#1357) * fix: remove left-over unnecessary code * Removes hardcoded flags and more explicit output * Fix test md5
2022-03-03 09:01:39 +00:00
- path: output/adapterremoval/versions.yml
md5sum: fa621c887897da5a379c719399c17db7
new module: AdapterRemoval (#309) * add adapterremoval module * fix indentations * switch to process_medium * update docker tests * remove duplicated entry * fix line ending * Update software/adapterremoval/main.nf * Update software/adapterremoval/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
- name: adapterremoval test_adapterremoval_paired_end_collapse
Fix: removes hardcoded flags and 'custom' file output for AdapterRemoval (#1357) * fix: remove left-over unnecessary code * Removes hardcoded flags and more explicit output * Fix test md5
2022-03-03 09:01:39 +00:00
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
new module: AdapterRemoval (#309) * add adapterremoval module * fix indentations * switch to process_medium * update docker tests * remove duplicated entry * fix line ending * Update software/adapterremoval/main.nf * Update software/adapterremoval/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
tags:
- adapterremoval
files:
Refactor adapterremoval (#1491) * refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings
2022-04-04 19:40:35 +00:00
- path: output/adapterremoval/test.collapsed.fastq.gz
Adapterremoval glob fix (#1391) * fix: remove left-over unnecessary code * Partial fix for AR module output declarations * Remove `def` for prefix so useable in output block * Fix tests * Add adapterlist support * Fix tests after addition of adapter list
2022-03-14 06:32:21 +00:00
md5sum: ff956de3532599a56c3efe5369f0953f
Refactor adapterremoval (#1491) * refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings
2022-04-04 19:40:35 +00:00
- path: output/adapterremoval/test.collapsed.truncated.fastq.gz
- path: output/adapterremoval/test.discarded.fastq.gz
- path: output/adapterremoval/test.settings
Adapterremoval glob fix (#1391) * fix: remove left-over unnecessary code * Partial fix for AR module output declarations * Remove `def` for prefix so useable in output block * Fix tests * Add adapterlist support * Fix tests after addition of adapter list
2022-03-14 06:32:21 +00:00
md5sum: 7f0b2328152226e46101a535cce718b3
Refactor adapterremoval (#1491) * refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings
2022-04-04 19:40:35 +00:00
- path: output/adapterremoval/test.pair1.truncated.fastq.gz
Adapterremoval glob fix (#1391) * fix: remove left-over unnecessary code * Partial fix for AR module output declarations * Remove `def` for prefix so useable in output block * Fix tests * Add adapterlist support * Fix tests after addition of adapter list
2022-03-14 06:32:21 +00:00
md5sum: 683be19bc1c83008944b6b719bfa34e1
Refactor adapterremoval (#1491) * refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings
2022-04-04 19:40:35 +00:00
- path: output/adapterremoval/test.pair2.truncated.fastq.gz
Adapterremoval glob fix (#1391) * fix: remove left-over unnecessary code * Partial fix for AR module output declarations * Remove `def` for prefix so useable in output block * Fix tests * Add adapterlist support * Fix tests after addition of adapter list
2022-03-14 06:32:21 +00:00
md5sum: e6548fe061f3ef86368b26da930174d0
Fix: removes hardcoded flags and 'custom' file output for AdapterRemoval (#1357) * fix: remove left-over unnecessary code * Removes hardcoded flags and more explicit output * Fix test md5
2022-03-03 09:01:39 +00:00
- path: output/adapterremoval/versions.yml
Adapterremoval glob fix (#1391) * fix: remove left-over unnecessary code * Partial fix for AR module output declarations * Remove `def` for prefix so useable in output block * Fix tests * Add adapterlist support * Fix tests after addition of adapter list
2022-03-14 06:32:21 +00:00
md5sum: 78f589bb313c8da0147ca8ce77d7f3bf
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