Add linting-enabled preprocessing subworkflow and wire in

modules.json

@@ -341,7 +341,7 @@
                     },
                     "fastq_qc_trim_filter_setstrandedness": {
                         "branch": "master",
-                        "git_sha": "9082d6440bdffbb4f5d9bd9d753361933b3febcb",
+                        "git_sha": "34774b3e29b5cdb70c1e08ac7860765b795648e2",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_subsample_fq_salmon": {

nextflow.config

@@ -38,6 +38,9 @@ params {
     umi_discard_read           = null
     save_umi_intermeds         = false
 
+    // Linting
+    skip_linting               = false
+
     // Trimming
     trimmer                    = 'trimgalore'
     min_trimmed_reads          = 10000

nextflow_schema.json

@@ -411,7 +411,7 @@
                 },
                 "min_mapped_reads": {
                     "type": "number",
-                    "default": 5.0,
+                    "default": 5,
                     "fa_icon": "fas fa-percentage",
                     "description": "Minimum percentage of uniquely mapped reads below which samples are removed from further processing.",
                     "help_text": "Some downstream steps in the pipeline will fail if this threshold is too low."
@@ -456,14 +456,14 @@
                 "stranded_threshold": {
                     "type": "number",
                     "minimum": 0.5,
-                    "maximum": 1.0,
+                    "maximum": 1,
                     "default": 0.8,
                     "description": "The fraction of stranded reads that must be assigned to a strandedness for confident assignment. Must be at least 0.5."
                 },
                 "unstranded_threshold": {
                     "type": "number",
-                    "minimum": 0.0,
-                    "maximum": 1.0,
+                    "minimum": 0,
+                    "maximum": 1,
                     "default": 0.1,
                     "description": "The difference in fraction of stranded reads assigned to 'forward' and 'reverse' below which a sample is classified as 'unstranded'. By default the forward and reverse fractions must differ by less than 0.1 for the sample to be called as unstranded."
                 }
@@ -602,6 +602,11 @@
                     "fa_icon": "fas fa-compress-alt",
                     "description": "Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run."
                 },
+                "skip_linting": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-fast-forward",
+                    "description": "Skip linting checks during FASTQ preprocessing and filtering."
+                },
                 "skip_trimming": {
                     "type": "boolean",
                     "description": "Skip the adapter trimming step.",