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Update all subworkflows name#784

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maxulysse merged 44 commits intonf-core:devfrom
maxulysse:dev_subworkflows
Oct 13, 2022
Merged

Update all subworkflows name#784
maxulysse merged 44 commits intonf-core:devfrom
maxulysse:dev_subworkflows

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@maxulysse maxulysse commented Oct 10, 2022 •
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Thanks to @scorreard for helping out figuring out all the new names:

bam_compress_samtools is the new bam_to_cram
bam_convert_samtools is the new alignment_to_fastq
bam_cram_applybqsr_spark is the new gatk4/recalibrate_spark
bam_cram_applybqsr is the new gatk4/recalibrate
bam_cram_baserecalibrator_spark is the new gatk4/prepare_recalibration_spark
bam_cram_baserecalibrator is the new gatk4/prepare_recalibration
bam_cram_joint_germline_variant_calling_gatk is the new gatk4/joint_germline_variant_calling
bam_cram_markduplicates_spark is the new gatk4/markduplicates_spark
bam_cram_markduplicates is the new gatk4/markduplicates
bam_cram_variant_calling_ascat is the new variantcalling/ascat
bam_cram_variant_calling_cnvkit is the new variantcalling/cnvkit
bam_cram_variant_calling_deepvariant is the new variantcalling/deepvariant
bam_cram_variant_calling_freebayes is the new variantcalling/freebayes
bam_cram_variant_calling_germline_manta is the new variantcalling/manta/germline
bam_cram_variant_calling_haplotypecaller is the new variantcalling/haplotypecaller
bam_cram_variant_calling_mpileup is the new variantcalling/mpileup
bam_cram_variant_calling_single_strelka is the new variantcalling/strelka/single
bam_cram_variant_calling_single_tiddit is the new variantcalling/tiddit/single
bam_cram_variant_calling_somatic_controlfreec is the new variantcalling/controlfreec/somatic
bam_cram_variant_calling_somatic_manta is the new variantcalling/manta/somatic
bam_cram_variant_calling_somatic_mutect2 is the new gatk4/tumor_normal_somatic_variant_calling
bam_cram_variant_calling_somatic_strelka is the new variantcalling/strelka/somatic
bam_cram_variant_calling_somatic_tiddit is the new variantcalling/tiddit/somatic
bam_cram_variant_calling_tumor_only_controlfreec is the new variantcalling/controlfreec/tumoronly
bam_cram_variant_calling_tumor_only_manta is the new variantcalling/manta/tumoronly
bam_cram_variant_calling_tumor_only_mutect2 is the new gatk4/tumor_only_somatic_variant_calling
bam_merge_index_samtools is the new merge_index_bam
cram_merge_index_samtools is the new merge_index_cram
cram_qc_mosdepth_samtools is the new cram_qc
fastq_align_bwamem_mem2_dragmap is the new gatk4/mapping
fastq_create_umi_consensus_fgbio is the new fgbio_create_umi_consensus
fastq_qc_fastqc is the new run_fastqc
vcf_annotate_ensemblvep is the new annotation/ensemblvep
vcf_annotate_snpeff is the new annotation/snpeff
vcf_qc_bcftools_vcftool is the new vcf_qc
vcf_variant_filtering_gatk is the new gatk4/single_sample_germline_variant_calling

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Oct 10, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 779de63

+| ✅ 154 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-10-12 22:47:55

@yuukiiwa yuukiiwa self-requested a review October 11, 2022 01:27
@maxulysse
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maxulysse commented Oct 11, 2022

Waiting for #735

@maxulysse maxulysse merged commit fd73fb0 into nf-core:dev Oct 13, 2022
@maxulysse maxulysse deleted the dev_subworkflows branch October 13, 2022 05:54
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@yuukiiwa yuukiiwa yuukiiwa approved these changes

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@maxulysse @FriederikeHanssen @yuukiiwa