Dev #24
Dev #24
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Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
add .fna support for pbmm2
Changing the names of the pbsv output
Co-authored-by: Felix Lenner <[email protected]>
fixing prefixing issue
update to version 1.0.1 for patch release
CHANGELOG.md
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| ## v1.0.1 - Sardine [02/26/2025] | ||
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| ### `Added` | ||
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| ### `Fixed` | ||
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| - Changed files produced downstream from PBSV to have an output file name containing 'pbsv' to indicate origin of the files | ||
| - Tweaks to the channels passed into HiPhase - specifically ensure that the inputted VCF and BAM channel are ordered in the same way (according to their shared meta). | ||
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New releases should go above the old release in the changelog
Also other convensions:
Put a link to the PR at the beginning of each entry and tag the person who made teh change, eg..
| ## v1.0.1 - Sardine [02/26/2025] | |
| ### `Added` | |
| ### `Fixed` | |
| - Changed files produced downstream from PBSV to have an output file name containing 'pbsv' to indicate origin of the files | |
| - Tweaks to the channels passed into HiPhase - specifically ensure that the inputted VCF and BAM channel are ordered in the same way (according to their shared meta). | |
| ## v1.0.1 - Sardine [02/26/2025] | |
| ### `Added` | |
| ### `Fixed` | |
| - [#19](https://github.com/nf-core/pacvar/pull/19) Changed files produced downstream from PBSV to have an output file name containing 'pbsv' to indicate origin of the files (by | |
| @tanyasarkjain) | |
| - Tweaks to the channels passed into HiPhase - specifically ensure that the inputted VCF and BAM channel are ordered in the same way (according to their shared meta). | |
workflows/pacvar.nf
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| bam_bai_vcf_snp_ch | ||
| .multiMap { meta, bam, bai, vcf, tbi -> | ||
| bam_bai: [meta, bam, bai] | ||
| vcf_tbi: [meta, vcf, tbi] | ||
| } | ||
| .set { orderd_bam_bai_vcf_tbi_snp } |
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As it look elsewhere you're using = for channel assignment I would do that everywhere for consistency instead of .set
| bam_bai_vcf_snp_ch | |
| .multiMap { meta, bam, bai, vcf, tbi -> | |
| bam_bai: [meta, bam, bai] | |
| vcf_tbi: [meta, vcf, tbi] | |
| } | |
| .set { orderd_bam_bai_vcf_tbi_snp } | |
| orderd_bam_bai_vcf_tbi_snp = bam_bai_vcf_snp_ch | |
| .multiMap { meta, bam, bai, vcf, tbi -> | |
| bam_bai: [meta, bam, bai] | |
| vcf_tbi: [meta, vcf, tbi] | |
| } |
workflows/pacvar.nf
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| bam_bai: [meta, bam, bai] | ||
| vcf_tbi: [meta, vcf, tbi] | ||
| } | ||
| .set { orderd_bam_bai_vcf_tbi_sv } |
docs/output.md
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| - `<basename>.phased.bam`: Haplotagged BAM - outputted from phasing based on SNV | ||
| - `<basename>.pbsv.phased.bam`: Haplotagged BAM - outputted from phasing based on SV | ||
| - `<basename>.phased.vcf`: The phased Variant File (SNV) (Zipped) | ||
| - `<basename>.pbsv.phased.vcf`: The phased Variant File (SV) (Zipped) | ||
| - `<basename>.stats.csv`: This CSV/TSV file contains information about the the phase blocks that were output by HiPhase (SNV) | ||
| - `<basename>.pbsv.stats.csv`: This CSV/TSV file contains information about the the phase blocks that were output by HiPhase (SV) |
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Now that I see this here: Would it make sense to set .snv. and .sv. to understand the different outputs from the filenames directly?
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I have resolved these comments in #25 which should contain all the changes suggested, if you could take a look. Further I see there is a conflict with nextflow.config, but due to permissions im unable to look and resolved the conflict myself - how should I go about this? Thanks! |
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@tanyasarkjain I've upgraded your repo permissions now (with great pwoer comes great responsbility!) Can you do it now? |
Co-authored-by: James A. Fellows Yates <[email protected]>
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@jfy133 Hi James! I still seem to be seeing the "dev is a protected branch" unfortunately and unable to click the "resolve conflicts" |
requested changes for 1.0.1 release
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@tanyasarkjain you need to do a manual merge, check the bottom of the box:
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PR checklist
nf-core pipelines 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).