Update the meta.yml of subworkflows

[mirpedrol]

The meta.yml of subworkflows should have the proper structure descirbing the structure of input and output channels.

A new flag --fix has been added to nf-core/tools v3.0.0 to help you restructure these files, but as the structure of channels can't be infered from the main.nf of the subworkflows, some manual work is required.

How To

1. Make sure to use nf-core/tools v3.0.0
2. Run the linting command with the --fix flag:

nf-core subworkflows lint --fix <subworkflow_name>

3. Manually update the information of input and output channels

You can have a look to an example PR updating some of the subworkflows for reference.

List of subworkflows

If you plan to work on updating one of the subworkflows, please edit this message and add your github handle next to it to assign it to you.

• bam_cnv_wisecondorx
• bam_create_som_pon_gatk
• bam_dedup_stats_samtools_umicollapse
• bam_dedup_stats_samtools_umitools
• bam_docounts_contamination_angsd
• bam_markduplicates_picard
• bam_markduplicates_samtools
• bam_ngscheckmate
• bam_qc_picard
• bam_rseqc
• bam_sort_stats_samtools
• bam_split_by_region
• bam_stats_mirna_mirtop
• bam_stats_samtools
• bam_subsampledepth_samtools
• bam_tumor_normal_somatic_variant_calling_gatk
• bam_tumor_normal_somatic_variant_calling_strelka
• bam_tumor_only_somatic_variant_calling_gatk
• bam_variant_calling_sort_freebayes_bcftools
• bam_variant_demix_boot_freyja
• bcl_demultiplex
• bed_scatter_bedtools
• bedgraph_bedclip_bedgraphtobigwig
• deepvariant
• fasta_binning_concoct
• fasta_build_add_kraken2
• fasta_build_add_kraken2_bracken
• fasta_clean_fcs
• fasta_explore_search_plot_tidk
• fasta_hmmsearch_rank_fastas
• fasta_index_dna
• fasta_newick_epang_gappa
• fastq_align_bamcmp_bwa
• fastq_align_bowtie2
• fastq_align_bwa
• fastq_align_bwaaln
• fastq_align_chromap
• fastq_align_dna
• fastq_align_hisat2
• fastq_align_mapad
• fastq_align_star
• fastq_contam_seqtk_kraken
• fastq_create_umi_consensus_fgbio
• fastq_download_prefetch_fasterqdump_sratools
• fastq_extract_kraken_krakentools
• fastq_fastqc_umitools_fastp
• fastq_fastqc_umitools_trimgalore
• fastq_find_mirna_mirdeep2
• fastq_ngscheckmate
• fastq_qc_trim_filter_setstrandedness
• fastq_subsample_fq_salmon
• fastq_taxonomic_profile_metaphlan
• fastq_trim_fastp_fastqc
• homer
• initialise
• mmseqs_contig_taxonomy
• multiple_impute_glimpse2
• preprocess_rnaseq
• quantify_pseudo_alignment
• utils_nextflow_pipeline
• utils_nfcore_pipeline
• utils_nfschema_plugin
• utils_nfvalidation_plugin
• vcf_annotate_ensemblvep
• vcf_annotate_ensemblvep_snpeff
• vcf_annotate_snpeff
• vcf_extract_relate_somalier
• vcf_gather_bcftools
• vcf_impute_glimpse
• vcf_phase_shapeit5