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nf-core
Repository to host tool-specific module files for the Nextflow DSL2 community!
## Check Documentation I have checked the following places for your error: - [x] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [x] [nf-core/module documentation](https://github.com/nf-core/modules/blob/master/README.md) ## Description of the bug Here doesn't show `log`...
Follow up to https://github.com/nf-core/modules/pull/1437#discussion_r834774713 We currently use `reads` for unaligned reads(`fastq`), and then `bam` for the aligned reads, but this doesn't cover `cram`, and `sam`. It also doesn't cover things...
I think it would be good to have a module for [LONGRANGER] - [x] This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command - [x] There is...
I think it would be good to have a module for [LONGRANGER] - [x] This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command - [x] There is...
## PR checklist Closes https://github.com/nf-core/modules/issues/905 - [x] This comment contains a description of changes (with reason). - [x] If you've fixed a bug or added code that should be tested,...
Please submit PRs fixing these modules to my fork: https://github.com/drpatelh/nf-core-modules/tree/update You should be able to run `pytest` as normal but the options are now in a `nextflow.config` like [here](https://github.com/drpatelh/nf-core-modules/blob/update/tests/modules/star/align/nextflow.config) instead...
Follow up to #1405 ``` =================================== FAILURES =================================== _________________________________ test session _________________________________ Observed md5sum '3723f143966441811779f643482d2a39' not equal to expected md5sum '875863b402f67403dac63ef59b9c9a8a' for file '/home/runner/pytest_workflow_02mk3r0x/faqcs_test_fastp_single_end/output/faqcs/test.trimmed.fastq.gz' _________________________________ test session _________________________________ Observed md5sum...
Follow up to #1405 ``` ───────┬──────────────────────────────────────────────────────────────────────── │ File: /home/runner/pytest_workflow_swc64_9s/gatk4_genotypegvcfs_test_gatk4_genotypegvcfs_gendb_input/log.out ───────┼──────────────────────────────────────────────────────────────────────── 1 │ N E X T F L O W ~ version 21.10.6 2 │ Launching `./tests/modules/gatk4/genotypegvcfs/main.nf` [desperate_engelbart] - revision:...
Follow up to #1405 **Only the conda tests fail**, singularity and docker both pass so I'm guessing it's an error with the package version in conda. ``` =================================== FAILURES ===================================...
Follow up to #1405 Probably the same thing as #1416 ``` =================================== FAILURES =================================== _________________________________ test session _________________________________ Observed md5sum '05dd5b3714358ec75d78f72b2729c963' not equal to expected md5sum 'babdfc2a3940a1e32a63479db2c1d600' for file '/home/runner/pytest_workflow_r6zhm_9y/seqtk_rename_test_seqtk_rename_fq/output/seqtk/test.renamed.fastq.gz'...