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Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
nf-core · Jul 24, 2024 · 39c8688 · 39c8688
1 parent 7a93c64
commit 39c8688
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -6,7 +6,7 @@
     "type": "object",
     "definitions": {
         "workflow_options": {
-            "title": "Workflow options",
+            "title": "Partial run options",
             "type": "object",
             "description": "",
             "default": "",
@@ -76,23 +76,23 @@
                 },
                 "save_trimmed_fail": {
                     "type": "boolean",
-                    "description": "Specify true to save files that failed to pass trimming thresholds ending in *.fail.fastq.gz"
+                    "description": "Specify `true` to save files that failed to pass trimming thresholds ending in *.fail.fastq.gz"
                 },
                 "save_merged": {
                     "type": "boolean",
                     "description": "Specify true to save all merged reads to the a file ending in *.merged.fastq.gz"
                 },
                 "skip_fastp": {
                     "type": "boolean",
-                    "description": "Skip the fastp process if true"
+                    "description": "Skip the fastp process if `true`"
                 },
                 "skip_fastqc": {
                     "type": "boolean",
                     "description": "Skip FastQC processes if true"
                 },
                 "extra_fastp_args": {
                     "type": "string",
-                    "description": "Extra arguements for fastp. For example, '--trim_front1 15 --trim_front2 15 --trim_tail1 5 --trim_tail2 5'"
+                    "description": "Extra arguements for fastp. For example, `--trim_front1 15 --trim_front2 15 --trim_tail1 5 --trim_tail2 5{:bash}`"
                 }
             },
             "fa_icon": "fas fa-cut"
@@ -128,19 +128,19 @@
                 "assemblers": {
                     "type": "string",
                     "default": "trinity,rnaspades",
-                    "description": "Assemblers to use. Possible options include \"trinity\", \"trinity_no_norm\" (trinity without normalized reads), and \"rnaspades\"."
+                    "description": "Assemblers to use. Possible options include `trinity`, `trinity_no_norm` (trinity without normalized reads), and `rnaspades`."
                 },
                 "extra_trinity_args": {
                     "type": "string",
                     "description": "Extra arguments to pass to Trinity command in addition to defaults. Applies to both trinity and trinity_no_norm."
                 },
                 "soft_filtered_transcripts": {
                     "type": "boolean",
-                    "description": "For including hard filtered transcripts (in addition to medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds."
+                    "description": "Include hard filtered transcripts (in addition to medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds."
                 },
                 "hard_filtered_transcripts": {
                     "type": "boolean",
-                    "description": "For including soft filtered transcripts (in addition to the medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds."
+                    "description": "Include soft filtered transcripts (in addition to the medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds."
                 },
                 "ss": {
                     "type": "string",
@@ -168,7 +168,7 @@
                 "busco_lineage": {
                     "type": "string",
                     "default": "auto",
-                    "description": "The BUSCO lineage to use, or \\\"auto\\\" to automatically select lineage\""
+                    "description": "The BUSCO lineage to use, or `auto` to automatically select lineage"
                 },
                 "busco_lineages_path": {
                     "type": "string",
@@ -227,7 +227,7 @@
                 "lib_type": {
                     "type": "string",
                     "default": "A",
-                    "description": "Override library type inferred based on strandedness defined in meta object. 'A' for auto."
+                    "description": "Override library type inferred based on strandedness defined in meta object. `A` for auto."
                 }
             },
             "fa_icon": "fas fa-fish"

diff --git a/subworkflows/local/utils_nfcore_denovotranscript_pipeline/main.nf b/subworkflows/local/utils_nfcore_denovotranscript_pipeline/main.nf
@@ -157,7 +157,7 @@ workflow PIPELINE_COMPLETION {
 def validateInputParameters() {
 
     if ( params.qc_only && params.skip_assembly ) {
-        error("Incompatible parameters: cannot use --skip_assembly and --QC_only modes together.")
+        error("Incompatible parameters: cannot use --skip_assembly and --qc_only modes together.")
     }
 
     if ( params.skip_assembly && !params.transcript_fasta ) {