Multiple tweaks #13
Multiple tweaks #13
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| #!/usr/bin/env python3 | |||
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| # Written by Igor Trujnara, released under the MIT license | |||
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Not sure if this is needed in each single script since the repository already has the MIT license and your attribution could be found in the README
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The checklist mentions this, and I saw some pipelines (e.g. rnaseq) do this, so I put those notes there just in case
| TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz, | ||
| TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, | ||
| id,query | ||
| BicD2,Q8TD16 |
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Maybe show here that is also to provide a path to a FASTA file?
nextflow_schema.json
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| @@ -113,11 +113,11 @@ | |||
| "help_text": "If `local_databases` is set to `true`, the pipeline will use this path to the PANTHER database.", | |||
| "fa_icon": "fas fa-database" | |||
| }, | |||
| "use_inspector": { | |||
| "skip_inspector": { | |||
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I would rename it to --skip_orthoinspector
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Renamed, along with other related params. I have not renamed the modules and channels, as they are not user-facing anyway and the names are already long enough. Let me know if this is fine.
| ch_fasta = ch_seqinfo.map { [it[0], []] } | ||
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| if(params.skip_downstream) { | ||
| ch_seqhits = ch_seqinfo.map { [it[0], []] } |
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Sorry, probably I am missing something but why creating all these empty channels?
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These are there to ensure that the channels are populated even if the steps that normally generate them are skipped. If this is not done, the report module will not run with downstream analysis turned off, even partially. Is there a more nf-core-idiomatic way to achieve this?
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
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.README.mdis updated (including new tool citations and authors/contributors).