Merge branch 'update-precommit' into 'dev'

run precommit

See merge request epi2melabs/workflows/wf-clone-validation!180

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
         always_run: true
         pass_filenames: false
         additional_dependencies:
-          - epi2melabs>=0.0.48
+          - epi2melabs>=0.0.50
       - id: build_models
         name: build_models
         entry: datamodel-codegen --strict-nullable --base-class workflow_glue.results_schema_helpers.BaseModel --use-schema-description --disable-timestamp --input results_schema.yml --input-file-type openapi --output bin/workflow_glue/results_schema.py

README.md

@@ -25,12 +25,12 @@ In brief, this workflow will perform the following:
 Recommended requirements:
 
 + CPUs = 4
-+ memory = 8GB
++ Memory = 8GB
 
-Minimum requirement:
+Minimum requirements:
 
 + CPUs = 4
-+ memory = 4GB
++ Memory = 4GB
 
 Approximate run time: 6 minutes per sample for 10,000 reads
 
@@ -148,7 +148,7 @@ https://community.nanoporetech.com/docs/prepare/library_prep_protocols/plasmid-s
 
 ## Outputs
 
-Outputs files may be aggregated including information for all             samples or provided per sample. Per sample files             will be prefixed with respective aliases and represented             below as {{ alias }}.
+Outputs files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}.
 
 | Title | File path | Description | Per sample or aggregated |
 |-------|-----------|-------------|--------------------------|

docs/03_compute_requirements.md

@@ -1,12 +1,12 @@
 Recommended requirements:
 
 + CPUs = 4
-+ memory = 8GB
++ Memory = 8GB
 
-Minimum requirement:
+Minimum requirements:
 
 + CPUs = 4
-+ memory = 4GB
++ Memory = 4GB
 
 Approximate run time: 6 minutes per sample for 10,000 reads
 

docs/07_outputs.md

@@ -1,4 +1,4 @@
-Outputs files may be aggregated including information for all             samples or provided per sample. Per sample files             will be prefixed with respective aliases and represented             below as {{ alias }}.
+Outputs files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}.
 
 | Title | File path | Description | Per sample or aggregated |
 |-------|-----------|-------------|--------------------------|

lib/NfcoreSchema.groovy

@@ -141,7 +141,7 @@ class NfcoreSchema {
         for (specifiedParam in params.keySet()) {
             // nextflow params
             if (nf_params.contains(specifiedParam)) {
-                log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
+                log.error "You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
                 has_error = true
             }
             // unexpected params
@@ -180,7 +180,7 @@ class NfcoreSchema {
             schema.validate(params_json)
         } catch (ValidationException e) {
             println ''
-            log.error 'ERROR: Validation of pipeline parameters failed!'
+            log.error 'Validation of pipeline parameters failed!'
             JSONObject exceptionJSON = e.toJSON()
             HashSet<String> observed_exceptions = []
             printExceptions(exceptionJSON, params_json, log, enums, raw_schema, observed_exceptions)

lib/ingress.nf

@@ -240,6 +240,7 @@ process checkBamHeaders {
     label "ingress"
     label "wf_common"
     cpus 1
+    memory "2 GB"
     input: tuple val(meta), path("input_dir/reads*.bam")
     output:
         // set the two env variables by `eval`-ing the output of the python script
@@ -257,6 +258,7 @@ process mergeBams {
     label "ingress"
     label "wf_common"
     cpus 3
+    memory "4 GB"
     input: tuple val(meta), path("input_bams/reads*.bam")
     output: tuple val(meta), path("reads.bam")
     shell:
@@ -271,6 +273,7 @@ process catSortBams {
     label "ingress"
     label "wf_common"
     cpus 4
+    memory "4 GB"
     input: tuple val(meta), path("input_bams/reads*.bam")
     output: tuple val(meta), path("reads.bam")
     script:
@@ -285,6 +288,7 @@ process sortBam {
     label "ingress"
     label "wf_common"
     cpus 3
+    memory "4 GB"
     input: tuple val(meta), path("reads.bam")
     output: tuple val(meta), path("reads.sorted.bam")
     script:
@@ -298,6 +302,7 @@ process bamstats {
     label "ingress"
     label "wf_common"
     cpus 3
+    memory "4 GB"
     input:
         tuple val(meta), path("reads.bam")
     output:
@@ -414,6 +419,7 @@ process move_or_compress_fq_file {
     label "ingress"
     label "wf_common"
     cpus 1
+    memory "2 GB"
     input:
         // don't stage `input` with a literal because we check the file extension
         tuple val(meta), path(input)
@@ -439,6 +445,7 @@ process fastcat {
     label "ingress"
     label "wf_common"
     cpus 3
+    memory "2 GB"
     input:
         tuple val(meta), path("input")
         val extra_args
@@ -737,6 +744,7 @@ process validate_sample_sheet {
     cpus 1
     label "ingress"
     label "wf_common"
+    memory "2 GB"
     input:
         path "sample_sheet.csv"
         val required_sample_types