Fix EClint errors

modules/nf-core/bamstats/generalstats/main.nf

@@ -48,4 +48,3 @@ process BAMSTATS_GENERALSTATS {
     END_VERSIONS
     """
 }
-

modules/nf-core/cat/cat/main.nf

@@ -76,4 +76,3 @@ def getFileSuffix(filename) {
     def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/
     return match ? match[0][1] : filename.substring(filename.lastIndexOf('.'))
 }
-

modules/nf-core/ensemblvep/filtervep/main.nf

@@ -47,4 +47,3 @@ process ENSEMBLVEP_FILTERVEP {
     END_VERSIONS
     """
 }
-

modules/nf-core/famsa/guidetree/main.nf

@@ -46,4 +46,3 @@ process FAMSA_GUIDETREE {
     END_VERSIONS
     """
 }
-

modules/nf-core/faqcs/main.nf

@@ -132,4 +132,3 @@ process FAQCS {
         END_VERSIONS
     """
 }
-

modules/nf-core/fgbio/sortbam/main.nf

@@ -33,4 +33,3 @@ process FGBIO_SORTBAM {
     END_VERSIONS
     """
 }
-

modules/nf-core/fqtk/main.nf

@@ -45,4 +45,3 @@ process FQTK {
         fqtk: \$(echo \$(fqtk --version 2>&1) | cut -d " " -f2)
     """
 }
-

modules/nf-core/icountmini/sigxls/main.nf

@@ -47,4 +47,3 @@ process ICOUNTMINI_SIGXLS {
     END_VERSIONS
     """
 }
-

modules/nf-core/kaiju/kaiju2krona/main.nf

@@ -49,4 +49,3 @@ process KAIJU_KAIJU2KRONA {
     END_VERSIONS
     """
 }
-

modules/nf-core/leviosam2/lift/main.nf

@@ -49,4 +49,3 @@ process LEVIOSAM2_LIFT {
     END_VERSIONS
     """
 }
-

modules/nf-core/metaphlan/makedb/main.nf

@@ -49,5 +49,3 @@ process METAPHLAN_MAKEDB {
     END_VERSIONS
     """
 }
-
-

modules/nf-core/plink/ld/main.nf

@@ -94,4 +94,3 @@ process PLINK_LD {
     END_VERSIONS
     """
 }
-

modules/nf-core/sniffles/main.nf

@@ -37,4 +37,3 @@ process SNIFFLES {
     END_VERSIONS
     """
 }
-

modules/nf-core/tcoffee/seqreformat/main.nf

@@ -46,5 +46,3 @@ process TCOFFEE_SEQREFORMAT {
     END_VERSIONS
     """
 }
-
-

subworkflows/nf-core/bam_cnv_wisecondorx/main.nf

@@ -38,4 +38,3 @@ workflow BAM_CNV_WISECONDORX {
 
     versions        = ch_versions                               // channel: path(versions.yml)
 }
-

subworkflows/nf-core/bam_docounts_contamination_angsd/main.nf

@@ -33,4 +33,3 @@ workflow BAM_DOCOUNTS_CONTAMINATION_ANGSD {
     txt      = ANGSD_CONTAMINATION.out.txt // channel: [ val(meta), [ txt ] ]
     versions = ch_versions                 // channel: [ path(versions.yml) ]
 }
-

subworkflows/nf-core/bam_ngscheckmate/main.nf

@@ -46,4 +46,3 @@ workflow BAM_NGSCHECKMATE {
     versions     = ch_versions                       // channel: [ versions.yml ]
 
 }
-

subworkflows/nf-core/bam_split_by_region/main.nf

@@ -65,4 +65,3 @@ workflow BAM_SPLIT_BY_REGION {
     bam_bai     = ch_output                         // channel: [ val(meta), path(bam), path(bai) ]
     versions    = ch_versions                       // channel: [ path(versions.yml) ]
 }
-

subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/main.nf

@@ -34,4 +34,3 @@ workflow BAM_VARIANT_CALLING_SORT_FREEBAYES_BCFTOOLS {
 
     versions = ch_versions                     // channel: [ path(versions.yml) ]
 }
-

subworkflows/nf-core/bam_variant_demix_boot_freyja/main.nf

@@ -78,4 +78,3 @@ workflow BAM_VARIANT_DEMIX_BOOT_FREYJA {
     lineages_meta  = ch_lineages_meta              // channel: [ path(lineages_meta) ]
     versions       = ch_versions                   // channel: [ path(versions.yml) ]
     }
-

subworkflows/nf-core/bed_scatter_bedtools/main.nf

@@ -29,4 +29,3 @@ workflow BED_SCATTER_BEDTOOLS {
 
     versions        = ch_versions       // channel: [ path(versions.yml) ]
 }
-

subworkflows/nf-core/fasta_binning_concoct/main.nf

@@ -53,4 +53,3 @@ workflow FASTA_BINNING_CONCOCT {
 
     versions = ch_versions                                         // channel: [ versions.yml ]
 }
-

subworkflows/nf-core/fasta_build_add_kraken2/main.nf

@@ -24,4 +24,3 @@ workflow FASTA_BUILD_ADD_KRAKEN2 {
     db = KRAKEN2_BUILD.out.db // channel: [ val(meta), [ db ] ]
     versions = ch_versions    // channel: [ versions.yml ]
 }
-

subworkflows/nf-core/fasta_build_add_kraken2_bracken/main.nf

@@ -39,4 +39,3 @@ workflow FASTA_BUILD_ADD_KRAKEN2_BRACKEN {
     db = ch_final_db // channel: [ val(meta), [ db ] ]
     versions = ch_versions    // channel: [ versions.yml ]
 }
-

subworkflows/nf-core/fasta_clean_fcs/main.nf

@@ -26,4 +26,3 @@ workflow FASTA_CLEAN_FCS {
     fcsgx_taxonomy_report       = FCS_FCSGX.out.taxonomy_report             // channel: [ val(meta), [ taxonomy_report ] ]
     versions                    = ch_versions                               // channel: [ versions.yml ]
 }
-

subworkflows/nf-core/fastq_align_bwaaln/main.nf

@@ -109,4 +109,3 @@ workflow FASTQ_ALIGN_BWAALN {
 
     versions = ch_versions         // channel: [ path(versions.yml) ]
 }
-

subworkflows/nf-core/fastq_align_hisat2/main.nf

@@ -41,4 +41,3 @@ workflow FASTQ_ALIGN_HISAT2 {
 
     versions = ch_versions                          // channel: [ versions.yml ]
 }
-

subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf

@@ -203,4 +203,3 @@ workflow FASTQ_CREATE_UMI_CONSENSUS_FGBIO {
     mappedconsensusbam = SORTBAM.out.bam                // channel: [ val(meta), [ bam ] ]
     versions           = ch_versions                    // channel: [ versions.yml ]
 }
-

subworkflows/nf-core/fastq_extract_kraken_krakentools/main.nf

@@ -23,4 +23,3 @@ workflow FASTQ_EXTRACT_KRAKEN_KRAKENTOOLS {
     multiqc_files = KRAKEN2_KRAKEN2.out.report                                           // channel: [ val(meta), path ]
     versions = ch_versions                                                               // channel: [ versions.yml ]
 }
-

subworkflows/nf-core/fastq_ngscheckmate/main.nf

@@ -39,4 +39,3 @@ workflow FASTQ_NGSCHECKMATE {
     pdf          = NGSCHECKMATE_VAFNCM.out.pdf          // channel: [ meta, pdf ], optional
     versions     = ch_versions                          // channel: [ versions.yml ]
 }
-

subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/main.nf

@@ -26,4 +26,3 @@ workflow FASTQ_TAXONOMIC_PROFILE_METAPHLAN {
 
     versions = ch_versions
 }
-

subworkflows/nf-core/mmseqs_contig_taxonomy/main.nf

@@ -53,4 +53,3 @@ workflow MMSEQS_CONTIG_TAXONOMY {
     db_contig   = ch_taxonomy_querydb       // channel: [ val(meta), db ]
     versions    = ch_versions               // channel: [ versions.yml ]
 }
-

subworkflows/nf-core/preprocess_rnaseq/main.nf

@@ -267,5 +267,3 @@ workflow PREPROCESS_RNASEQ {
     multiqc_files   = ch_multiqc_files.transpose().map{it[1]}
     versions        = ch_versions                     // channel: [ versions.yml ]
 }
-
-

subworkflows/nf-core/vcf_gather_bcftools/main.nf

@@ -42,4 +42,3 @@ workflow VCF_GATHER_BCFTOOLS {
 
     versions = ch_versions           // channel: [ versions.yml ]
 }
-

subworkflows/nf-core/vcf_phase_shapeit5/main.nf

@@ -93,4 +93,3 @@ workflow VCF_PHASE_SHAPEIT5 {
     variants_index      = VCF_INDEX2.out.csi                     // channel: [ val(meta), csi ]
     versions            = ch_versions                            // channel: [ versions.yml ]
 }
-