Plan for migrating sarek to accordance with Nextflow LS

[maxulysse]

The plan - One Step At A Time

Errors

• modules
  • [x] local
  • [ ] nf-core - need to pull in the new changes
    • [ ] msisensorpro/msisomatic
      • [x] https://github.com/nf-core/sarek/pull/1965
    • [x] sentieon/varcal
      • [x] https://github.com/nf-core/sarek/pull/1977
    • [ ] unzip
      • [ ] https://github.com/nf-core/modules/pull/8924
• subworkflows
  • [ ] local
    • [ ] subworkflows/local/bam_applybqsr/main.nf
    • [ ] subworkflows/local/bam_applybqsr_spark/main.nf
    • [ ] subworkflows/local/bam_baserecalibrator/main.nf
    • [ ] subworkflows/local/bam_baserecalibrator_spark/main.nf
    • [ ] subworkflows/local/bam_joint_calling_germline_gatk/main.nf
    • [ ] subworkflows/local/bam_joint_calling_germline_sentieon/main.nf
    • [ ] subworkflows/local/bam_markduplicates/main.nf
    • [ ] subworkflows/local/bam_markduplicates_spark/main.nf
    • [ ] subworkflows/local/bam_sentieon_dedup/main.nf
    • [ ] subworkflows/local/bam_variant_calling_deepvariant/main.nf
    • [ ] subworkflows/local/bam_variant_calling_germline_all/main.nf
    • [ ] subworkflows/local/bam_variant_calling_germline_manta/main.nf
    • [ ] subworkflows/local/bam_variant_calling_haplotypecaller/main.nf
    • [ ] subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf
    • [ ] subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf
    • [ ] subworkflows/local/bam_variant_calling_single_strelka/main.nf
    • [ ] subworkflows/local/bam_variant_calling_somatic_manta/main.nf
    • [ ] subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf
    • [ ] subworkflows/local/bam_variant_calling_somatic_strelka/main.nf
    • [ ] subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
    • [ ] subworkflows/local/bam_variant_calling_tumor_only_lofreq/main.nf
    • [ ] subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf
    • [ ] subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf
    • [ ] subworkflows/local/channel_align_create_csv/main.nf
    • [ ] subworkflows/local/channel_applybqsr_create_csv/main.nf
    • [ ] subworkflows/local/channel_baserecalibrator_create_csv/main.nf
    • [ ] subworkflows/local/channel_markduplicates_create_csv/main.nf
    • [ ] subworkflows/local/channel_variant_calling_create_csv/main.nf
    • [ ] subworkflows/local/cram_merge_index_samtools/main.nf
    • [ ] subworkflows/local/fastq_align/main.nf
    • [ ] subworkflows/local/prepare_genome/main.nf
      • [ ] https://github.com/nf-core/sarek/pull/1979
    • [ ] subworkflows/local/prepare_intervals/main.nf
    • [ ] subworkflows/local/prepare_reference_cnvkit/main.nf
    • [ ] subworkflows/local/vcf_qc_bcftools_vcftools/main.nf
    • [ ] subworkflows/local/vcf_variant_filtering_gatk/main.nf
  • [x] nf-core
• workflows
  • [ ] sarek/main.nf
• root
  • [ ] main.nf
  • [ ] nextflow.config
• conf
  • [ ] basic confs
• [ ] whatever is left