added fair directive to all processes

phac-nml · Jun 5, 2024 · bb409b9 · bb409b9
1 parent df48c71
commit bb409b9
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diff --git a/modules/local/abricate.nf b/modules/local/abricate.nf
@@ -7,6 +7,7 @@ process ABRICATE {
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
 
+    fair true
     input:
     tuple val(meta), path(assembly)
 

diff --git a/modules/local/bakta_annotate.nf b/modules/local/bakta_annotate.nf
@@ -7,6 +7,7 @@ process BAKTA_ANNOTATE {
     label 'process_high'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(fasta)
     path db

diff --git a/modules/local/bandage_image.nf b/modules/local/bandage_image.nf
@@ -5,6 +5,7 @@ process BANDAGE_IMAGE {
     label "process_low"
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(gfa)
 

diff --git a/modules/local/bin_kraken2.nf b/modules/local/bin_kraken2.nf
@@ -10,6 +10,7 @@ process BIN_KRAKEN2{
     cache 'deep' // ! Deep caching is required to not bungle up the later metadata updates on resumes
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(contigs), path(kraken_report), path(kraken_output)
     val taxonomic_level

diff --git a/modules/local/check_ont.nf b/modules/local/check_ont.nf
@@ -10,6 +10,7 @@ process CHECK_ONT{
     // TODO perhaps reads should just be dedupped by header...
     // TODO Awk would be faster...
 
+    fair true
     input:
     tuple val(meta), path(reads)
 

diff --git a/modules/local/checkm_lineagewf.nf b/modules/local/checkm_lineagewf.nf
@@ -6,6 +6,7 @@ process CHECKM_LINEAGEWF {
     label 'process_high'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(fasta)
 

diff --git a/modules/local/chopper_trim.nf b/modules/local/chopper_trim.nf
@@ -6,6 +6,7 @@ process CHOPPER_TRIM{
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
 
+    fair true
     input:
     tuple val(meta), path(reads)
 

diff --git a/modules/local/combine_data.nf b/modules/local/combine_data.nf
@@ -5,6 +5,7 @@ process COMBINE_DATA{
     label "process_low"
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(fastq_1), path(fastq_2), path(long_reads), path(assembly)
 

diff --git a/modules/local/ectyper.nf b/modules/local/ectyper.nf
@@ -8,6 +8,7 @@ process ECTYPER{
     label 'process_medium'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(fasta)
 

diff --git a/modules/local/fastp_trim.nf b/modules/local/fastp_trim.nf
@@ -8,6 +8,7 @@ process FASTP_TRIM{
     label "process_medium" // fastp uses very little memory in reality, but for duplicate analysis it is better to give it more memory
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(reads)
 

diff --git a/modules/local/fastqscan.nf b/modules/local/fastqscan.nf
@@ -4,6 +4,7 @@ process FASTQSCAN {
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
 
+    fair true
     input:
     tuple val(meta), path(reads)
 

diff --git a/modules/local/flye_assemble.nf b/modules/local/flye_assemble.nf
@@ -13,6 +13,7 @@ process FLYE_ASSEMBLE{
     memory { task.memory * task.attempt}
     // TODO check if --debug flag should be added to flye to actually  turns off the debug logging?
 
+    fair true
     input:
     tuple val(meta), path(reads)
     val mode

diff --git a/modules/local/gzip_files.nf b/modules/local/gzip_files.nf
@@ -7,6 +7,7 @@ process GZIP_FILES {
     label 'process_low'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(file_in)
 

diff --git a/modules/local/kat_hist.nf b/modules/local/kat_hist.nf
@@ -10,6 +10,7 @@ process KAT_HIST{
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
 
+    fair true
     input:
     tuple val(meta), path(reads)
     val long_reads_p

diff --git a/modules/local/kleborate.nf b/modules/local/kleborate.nf
@@ -8,6 +8,7 @@ process KLEBORATE {
     label 'process_medium'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(fastas)
 

diff --git a/modules/local/kraken.nf b/modules/local/kraken.nf
@@ -6,6 +6,7 @@ process KRAKEN {
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
 
+    fair true
     input:
     tuple val(meta), path(contigs)
     path db

diff --git a/modules/local/lissero.nf b/modules/local/lissero.nf
@@ -11,6 +11,7 @@ process LISSERO {
     // TODO add in log message saying what went wrong with the sample
     errorStrategy 'ignore' // TODO set a proper strategy once the issues with the mash parsing script are solved e.g. the ambiguous top hits
 
+    fair true
     input:
     tuple val(meta), path(fasta)
 

diff --git a/modules/local/locidex_extract.nf b/modules/local/locidex_extract.nf
@@ -10,6 +10,7 @@ process LOCIDEX_EXTRACT {
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
 
+    fair true
     input:
     tuple val(meta), path(fasta), path(db)
 

diff --git a/modules/local/locidex_report.nf b/modules/local/locidex_report.nf
@@ -7,6 +7,7 @@ process LOCIDEX_REPORT {
     label "process_low"
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(seq_store)
 

diff --git a/modules/local/locidex_search.nf b/modules/local/locidex_search.nf
@@ -9,6 +9,7 @@ process LOCIDEX_SEARCH {
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
 
+    fair true
     input:
     tuple val(meta), path(fasta), path(db)
 

diff --git a/modules/local/mash_estimate.nf b/modules/local/mash_estimate.nf
@@ -8,6 +8,7 @@ process MASH_ESTIMATE{
     tag "${prefix}"
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(reads)
     val long_reads_p

diff --git a/modules/local/mash_paste.nf b/modules/local/mash_paste.nf
@@ -5,6 +5,7 @@ process MASH_PASTE{
     label 'process_low'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(sketches) // getting all output sketches
 

diff --git a/modules/local/mash_screen.nf b/modules/local/mash_screen.nf
@@ -10,6 +10,7 @@ process MASH_SCREEN {
     label 'process_medium'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(reads)
     path sequences_sketch

diff --git a/modules/local/mash_sketch.nf b/modules/local/mash_sketch.nf
@@ -6,6 +6,7 @@ process MASH_SKETCH{
     label 'process_low'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(fasta), val(comment)
 

diff --git a/modules/local/medaka_polish.nf b/modules/local/medaka_polish.nf
@@ -8,6 +8,7 @@ process MEDAKA_POLISH{
     beforeScript 'rm -rf medaka' // Same reasoning as above
     errorStrategy { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' } // May be having issues with medaka model copying
 
+    fair true
     input:
     tuple val(meta), path(reads), path(assembly)
     val model

diff --git a/modules/local/minimap2_index.nf b/modules/local/minimap2_index.nf
@@ -5,6 +5,7 @@ process MINIMAP2_INDEX{
     label 'process_low'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(contigs)
 

diff --git a/modules/local/minimap2_map.nf b/modules/local/minimap2_map.nf
@@ -7,6 +7,7 @@ process MINIMAP2_MAP {
     label 'process_medium'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(reads), path(index), path(contigs)
     val paf_out

diff --git a/modules/local/mlst.nf b/modules/local/mlst.nf
@@ -5,6 +5,7 @@ process MLST {
     label "process_low"
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(fasta)
 

diff --git a/modules/local/mob_recon.nf b/modules/local/mob_recon.nf
@@ -6,6 +6,7 @@ process MOBSUITE_RECON {
 
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(fasta)
 

diff --git a/modules/local/parse_fastp.nf b/modules/local/parse_fastp.nf
@@ -5,6 +5,7 @@ process PARSE_FASTP{
     tag "$meta.id"
     label "process_single"
 
+    fair true
     input:
     tuple val(meta), val(json)
 

diff --git a/modules/local/parse_kat.nf b/modules/local/parse_kat.nf
@@ -7,6 +7,7 @@ process PARSE_KAT {
     label "process_single"
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), val(json)
 

diff --git a/modules/local/parse_kraken.nf b/modules/local/parse_kraken.nf
@@ -5,6 +5,7 @@ process PARSE_KRAKEN {
     label "process_low"
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(kraken_report)
 

diff --git a/modules/local/parse_mash.nf b/modules/local/parse_mash.nf
@@ -8,6 +8,7 @@ process PARSE_MASH{
     label "process_low"
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(mash_screen)
     val run_mode

diff --git a/modules/local/pilon_polish.nf b/modules/local/pilon_polish.nf
@@ -10,6 +10,7 @@ process PILON_POLISH {
 
 
     // NOTE some inputs not used, they are just there to maintain a common interface with other polishing programs
+    fair true
     input:
     tuple val(meta), path(reads), path(contigs), path(bam), path(bai) // may need to copy the bai into the work dir
 

diff --git a/modules/local/pilon_polisher.nf b/modules/local/pilon_polisher.nf
@@ -6,6 +6,7 @@ process PILON_ITER {
     memory  {task.memory * task.attempt}
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(reads), path(contigs)
 

diff --git a/modules/local/quast_assembly.nf b/modules/local/quast_assembly.nf
@@ -7,6 +7,7 @@ process QUAST {
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
 
+    fair true
     input:
     tuple val(meta), path(contigs), path(trimmed_reads)
 

diff --git a/modules/local/racon_polish.nf b/modules/local/racon_polish.nf
@@ -8,6 +8,7 @@ process RACON_POLISH {
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
     afterScript "rm ${input_reads}"
 
+    fair true
     input:
     tuple val(meta), path(reads), path(sam), path(contigs)
 

diff --git a/modules/local/read_summary.nf b/modules/local/read_summary.nf
@@ -7,6 +7,7 @@ process READ_SCAN{
     tag "${meta.id}"
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(reads), path(l_reads)
 

diff --git a/modules/local/remove_contaminants.nf b/modules/local/remove_contaminants.nf
@@ -5,6 +5,7 @@ process REMOVE_CONTAMINANTS {
     label 'process_medium'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(reads)
     path contaminant_fa

diff --git a/modules/local/report.nf b/modules/local/report.nf
@@ -13,6 +13,7 @@ process REPORT{
     tag "Report Generation"
     label "process_single"
 
+    fair true
     input:
     val test_in
 

diff --git a/modules/local/report_aggregate.nf b/modules/local/report_aggregate.nf
@@ -7,6 +7,7 @@ process REPORT_AGGREGATE{
     label 'process_medium'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     path summary_report
 

diff --git a/modules/local/sam_to_bam.nf b/modules/local/sam_to_bam.nf
@@ -6,6 +6,7 @@ process SAM_TO_BAM{
     label 'process_low'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(sam)
 

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
@@ -7,6 +7,7 @@ process SAMPLESHEET_CHECK {
         'https://depot.galaxyproject.org/singularity/python:3.8.3' :
         'quay.io/biocontainers/python:3.8.3' }"
 
+    fair true
     input:
     path samplesheet
 

diff --git a/modules/local/select_pointfinder.nf b/modules/local/select_pointfinder.nf
@@ -4,6 +4,7 @@ process IDENTIFY_POINTDB {
     tag "$meta.id"
     label "process_single"
 
+    fair true
     input:
     tuple val(meta), val(species)
 

diff --git a/modules/local/seqkit_filter.nf b/modules/local/seqkit_filter.nf
@@ -7,6 +7,7 @@ process SEQKIT_FILTER {
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
 
+    fair true
     input:
     tuple val(meta), path(contigs), path(reads)
     val min_length

diff --git a/modules/local/seqkit_stats.nf b/modules/local/seqkit_stats.nf
@@ -7,6 +7,7 @@ process SEQKIT_STATS {
     label 'process_single'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(contigs), path(trimmed_reads)
 

diff --git a/modules/local/seqtk_fasta_fastq.nf b/modules/local/seqtk_fasta_fastq.nf
@@ -7,6 +7,7 @@ process SEQTK_FASTA_FASTQ{
     label 'process_low'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(fasta)
 

diff --git a/modules/local/seqtk_sample.nf b/modules/local/seqtk_sample.nf
@@ -6,6 +6,7 @@ process SEQTK_SAMPLE{
     label "process_low"
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(reads), val(sample_fraction)
 

diff --git a/modules/local/seqtk_size.nf b/modules/local/seqtk_size.nf
@@ -3,6 +3,7 @@ process SEQTK_SIZE{
     label "process_low"
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(reads)
 

diff --git a/modules/local/shigatyper.nf b/modules/local/shigatyper.nf
@@ -8,6 +8,7 @@ process SHIGATYPER{
     label 'process_low'
     container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
 
+    fair true
     input:
     tuple val(meta), path(reads) // in mkkondo it will only work with assemblies