Merge dev to master #87
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Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
feat bumped up
adding closures to modules.config
trying to fix star_index channel cardinality
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
Solve some issues
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fevac
approved these changes
Mar 14, 2024
fellen31
approved these changes
Mar 15, 2024
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Looks good to me!
Although, one thing is I should be able to run the test profile with --variant_caller gatk right? I think there are some mismatches between what is given and what is expected as input to processes in that workflow. I think I have fixed it, but someone will have to tell me where it's appropriate for me to put these changes 😃
| ch_out_drop_as_tsv = DROP_CONFIG_RUN_AS.out.drop_as_tsv ? DROP_CONFIG_RUN_AS.out.drop_as_tsv.collect() | ||
| : Channel.empty() | ||
| ch_out_drop_ae_rds = DROP_CONFIG_RUN_AE.out.drop_ae_rds ? DROP_CONFIG_RUN_AE.out.drop_ae_rds.collect() | ||
| : Channel.empty() |
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| : Channel.empty() | |
| : Channel.of([]) |
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For consistency, I think its better to keek 'Channel.empty()' because it is what has been used in most instances, like at workflows/tomte.nf. If you want, we can also discuss ^^
| ch_out_drop_gene_name_as = DROP_CONFIG_RUN_AS.out.drop_gene_name ? DROP_CONFIG_RUN_AS.out.drop_gene_name.collect() | ||
| : Channel.empty() | ||
| ch_out_drop_as_tsv = DROP_CONFIG_RUN_AS.out.drop_as_tsv ? DROP_CONFIG_RUN_AS.out.drop_as_tsv.collect() | ||
| : Channel.empty() |
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| : Channel.empty() | |
| : Channel.of([]) |
| ch_gene_panel_clinical_filter, | ||
| ch_out_drop_ae_rds, | ||
| ch_out_drop_ae_rds.ifEmpty([]), |
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| ch_out_drop_ae_rds.ifEmpty([]), | |
| ch_out_drop_ae_rds, |
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Initially it was as you suggested but when either the ae or as is turned off, then the filtering is not run. To be honest, I am not sure what the difference is exactly, if you want to, we can discuss.
| ch_out_drop_gene_name, | ||
| ch_out_drop_as_tsv | ||
| ch_out_drop_as_tsv.ifEmpty([]) |
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| ch_out_drop_as_tsv.ifEmpty([]) | |
| ch_out_drop_as_tsv |
fix typos Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com>
Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
Lucpen
commented
Mar 15, 2024
Fix expected input for modules in the GATK subworkflow --------- Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
Add insert size calculation
Lucpen
added a commit
that referenced
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Mar 18, 2024
Merge pull request #87 from genomic-medicine-sweden/dev
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).