nf-core · maxulysse · Apr 27, 2023 · Apr 27, 2023
diff --git a/subworkflows/nf-core/bam_create_som_pon_gatk/meta.yml b/subworkflows/nf-core/bam_create_som_pon_gatk/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: bam_create_som_pon_gatk
 description: Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.
 keywords:

diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "bam_dedup_stats_samtools_umitools"
 description: UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats
 keywords:

diff --git a/subworkflows/nf-core/bam_docounts_contamination_angsd/meta.yml b/subworkflows/nf-core/bam_docounts_contamination_angsd/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "bam_docounts_contamination_angsd"
 description: Calculate contamination of the X-chromosome with ANGSD
 keywords:

diff --git a/subworkflows/nf-core/bam_markduplicates_picard/meta.yml b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "bam_markduplicates_picard"
 description: Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats
 keywords:

diff --git a/subworkflows/nf-core/bam_ngscheckmate/meta.yml b/subworkflows/nf-core/bam_ngscheckmate/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "bam_ngscheckmate"
 description: Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.
 keywords:

diff --git a/subworkflows/nf-core/bam_qc_picard/meta.yml b/subworkflows/nf-core/bam_qc_picard/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: bam_qc
 description: Produces comprehensive statistics from BAM file
 keywords:

diff --git a/subworkflows/nf-core/bam_rseqc/meta.yml b/subworkflows/nf-core/bam_rseqc/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: bam_rseqc
 description: Subworkflow to run multiple commands in the RSeqC package
 keywords:

diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: bam_sort_stats_samtools
 description: Sort SAM/BAM/CRAM file
 keywords:

diff --git a/subworkflows/nf-core/bam_split_by_region/meta.yml b/subworkflows/nf-core/bam_split_by_region/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "bam_split_by_region"
 description: Split the reads in the input bam by specified genomic region.
 keywords:

diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: bam_stats_samtools
 description: Produces comprehensive statistics from SAM/BAM/CRAM file
 keywords:

diff --git a/subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/meta.yml b/subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: bam_tumor_normal_somatic_variant_calling_gatk
 description: |
   Perform variant calling on a paired tumor normal set of samples using mutect2 tumor normal mode.

diff --git a/subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/meta.yml b/subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "bam_variant_calling_sort_freebayes_bcftools"
 description: Call variants using freebayes, then sort and index
 keywords:

diff --git a/subworkflows/nf-core/bam_variant_demix_boot_freyja/meta.yml b/subworkflows/nf-core/bam_variant_demix_boot_freyja/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "bam_variant_demix_boot_freyja"
 description: Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference)
 keywords:

diff --git a/subworkflows/nf-core/bcl_demultiplex/meta.yml b/subworkflows/nf-core/bcl_demultiplex/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "bcl_demultiplex"
 description: Demultiplex Illumina BCL data using bcl-convert or bcl2fastq
 keywords:

diff --git a/subworkflows/nf-core/bed_scatter_bedtools/meta.yml b/subworkflows/nf-core/bed_scatter_bedtools/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "bed_scatter_bedtools"
 description: |
   Scatters inputted BED files by the amount specified.

diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "bedgraph_bedclip_bedgraphtobigwig"
 description: Convert bedgraph to bigwig with clip
 keywords:

diff --git a/subworkflows/nf-core/fasta_binning_concoct/meta.yml b/subworkflows/nf-core/fasta_binning_concoct/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fasta_binning_concoct"
 description: Runs the CONCOCT workflow of contig binning
 keywords:

diff --git a/subworkflows/nf-core/fasta_index_dna/meta.yml b/subworkflows/nf-core/fasta_index_dna/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fasta_index_dna"
 description: |
   Generate aligner index for a reference genome.

diff --git a/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml b/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fasta_newick_epang_gappa"
 description: Run phylogenetic placement with a number of query sequences plus a reference alignment and phylogeny. Used in nf-core/phyloplace.
 keywords:

diff --git a/subworkflows/nf-core/fastq_align_bowtie2/meta.yml b/subworkflows/nf-core/fastq_align_bowtie2/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: fastq_align_bowtie2
 description: Align reads to a reference genome using bowtie2 then sort with samtools
 keywords:

diff --git a/subworkflows/nf-core/fastq_align_bwa/meta.yml b/subworkflows/nf-core/fastq_align_bwa/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: fastq_align_bwa
 description: Align reads to a reference genome using bwa then sort with samtools
 keywords:

diff --git a/subworkflows/nf-core/fastq_align_bwaaln/meta.yml b/subworkflows/nf-core/fastq_align_bwaaln/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fastq_align_bwaaln_samtools"
 description: Align FASTQ files against reference genome with the bwa aln short-read aligner producing a sorted and indexed BAM files
 keywords:

diff --git a/subworkflows/nf-core/fastq_align_chromap/meta.yml b/subworkflows/nf-core/fastq_align_chromap/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fastq_align_chromap"
 description: Align high throughput chromatin profiles using Chromap then sort with samtools
 keywords:

diff --git a/subworkflows/nf-core/fastq_align_dna/meta.yml b/subworkflows/nf-core/fastq_align_dna/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fastq_align_dna"
 description: Align fastq files to a reference genome
 keywords:

diff --git a/subworkflows/nf-core/fastq_align_hisat2/meta.yml b/subworkflows/nf-core/fastq_align_hisat2/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fastq_align_hisat2"
 description: Align reads to a reference genome using hisat2 then sort with samtools
 keywords:

diff --git a/subworkflows/nf-core/fastq_align_star/meta.yml b/subworkflows/nf-core/fastq_align_star/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fastq_align_star"
 description: Align reads to a reference genome using bowtie2 then sort with samtools
 keywords:

diff --git a/subworkflows/nf-core/fastq_contam_seqtk_kraken/meta.yml b/subworkflows/nf-core/fastq_contam_seqtk_kraken/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "FASTQ_CONTAM_SEQTK_KRAKEN"
 description: Produces a contamination report from FastQ input after subsampling
 keywords:

diff --git a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/meta.yml b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: fgbio_create_umi_consensus
 description: |
   This workflow uses the suite FGBIO to identify and remove UMI tags from FASTQ reads

diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: fastq_download_prefetch_fasterqdump_sratools
 description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
 keywords:

diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 # yaml-language-server: $schema=yaml-schema.json
 name: "fastq_fastqc_umitools_fastp"
 description: Read QC, UMI extraction and trimming

diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fastq_fastqc_umitools_trimgalore"
 description: Read QC, UMI extraction and trimming
 keywords:

diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml b/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fastq_subsample_fq_salmon"
 description: Subsample fastq
 keywords:

diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml b/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fastq_trim_fastp_fastqc"
 description: Read QC, fastp trimming and read qc
 keywords:

diff --git a/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/meta.yml b/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: gatk_tumor_only_somatic_variant_calling
 description: |
   Perform variant calling on a single tumor sample using mutect2 tumor only mode.

@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: vcf_annotate_ensemblvep
 description: Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file
 keywords:

@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: vcf_annotate_snpeff
 description: Perform annotation with snpEff and bgzip + tabix index the resulting VCF file
 keywords:

diff --git a/subworkflows/nf-core/vcf_extract_relate_somalier/meta.yml b/subworkflows/nf-core/vcf_extract_relate_somalier/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "vcf_extract_relate_somalier"
 description: Perform somalier extraction and relate stats on input VCFs
 keywords:

diff --git a/subworkflows/nf-core/vcf_gather_bcftools/meta.yml b/subworkflows/nf-core/vcf_gather_bcftools/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "vcf_gather_bcftools"
 description: |
   Concatenate several VCF files using bcftools concat.

diff --git a/subworkflows/nf-core/vcf_impute_glimpse/meta.yml b/subworkflows/nf-core/vcf_impute_glimpse/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "vcf_imputation_glimpse"
 description: Impute VCF/BCF files with Glimpse
 keywords:

diff --git a/subworkflows/nf-core/vcf_phase_shapeit5/meta.yml b/subworkflows/nf-core/vcf_phase_shapeit5/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "vcf_phase_shapeit5"
 description: Phase vcf panel with Shapeit5 tools
 keywords: