nf-core_modules/tests/modules/samtools
Edmund Miller c19671dca9
Subworkflow Infrastructure (#662)
* feat(subworkflows): Add align_bowtie2 subworkflow

For testing CI setup

* test(align_bowtie2): Add initial list of changes to test

* test(align_bowtie2): Add initial test

* refactor: Use tags to run subworkflows ci

For every underlying module used by workflow and allow the modules
pytest-modules definition be the source of truth.

* refactor: Use individual directories for subworkflows

* docs(align_bowtie2): Add initial meta.yml

Copied most of it from the bowtie2/align module.

* fix(align_bowtie2): Fix module include paths

* test(bam_sort_samtools): Add initial test

* ci(bam_sort_samtools): Add modules that trigger the tag

* test(bam_stats_samtools): Add initial test

* ci(bam_stats_samtools): Add keys to pick up changes

* docs(bam_samtools): Add initial meta.yml

* test(align_bowtie2): Fix path to subworkflow

* test(align_bowtie2): Update entry point

* fix(bam_sort_samtools): Update include paths

* test(bam_sort_samtools): Fix path

* style: Clean up addParams

* test(samtools_sort): Add suffix for test

* test(align_bowtie2): Add samtools_options for suffix

* test(bam_stats_samtools): Update path

* test(bam_stats_samtools): Use stats input

Otherwise it's just an example of how it's used in the bam_sort_samtools subworkflow

* ci(linting): Skip module linting of subworkflows

* ci(linting): Clean up startsWith statement

* test(bam_stats_samtools): Use single end test data for single end test

* test(bam_stats_samtools): Add expected files

* test(align_bowtie2): Add paired-end test

* test(align_bowtie2): Sort order of output

* test(align_bowtie2): Update hashes

* docs(align_bowtie2): Fix typo

* test(align_bowtie2): Update samtools output names

* test(align_bowtie2): Remove md5sums for bam/bai

* feat(subworkflows): Add nextflow.configs

These can be used for default settings in the future. They can then be
included in the conf/modules.config so that the params don't have to be
duplicated in the root nextflow.config.

* docs(subworkflows): Include modules instead of tools

* fix: Update to versions

* chore(align_bowtie2): Remove duplicate tag

* style: Format yamls

* test(subworkflows): Only check versions for modules

* chore: Update subworkflows to match rnaseq dev

* fix(subworkflows): Update paths

* fix(bam_sort_samtools): Fix sort parameters for testing

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* docs: Update TODOs with a message

* ci: Try using a matrix for strategy

* ci: Try passing an array

* Revert "ci: Try passing an array"

This reverts commit d3611fcd8332bbb9a8501e8dd299d0a623aaecaa.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-08 16:02:42 +01:00
..
ampliconclip Add samtools ampliconclip (#590) 2021-07-20 21:31:31 +01:00
faidx Fix version commands (#749) 2021-09-27 22:10:37 +01:00
fastq nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
flagstat nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
idxstats Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
index Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
merge fix: update samtools_merge (#582) 2021-07-16 14:32:17 +02:00
mpileup nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
sort Subworkflow Infrastructure (#662) 2021-10-08 16:02:42 +01:00
stats nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
view Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00