Merge pull request #14 from a4000/dev

Small improvements to documentation, test_full, and a few processes
nf-core · Nov 17, 2023 · 56a7d3f · 56a7d3f
2 parents 7649160 + 79d6e39
commit 56a7d3f
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Showing 4 changed files with 24 additions and 20 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -73,7 +73,7 @@ process {
     }
 
     withName: CRABS_DBIMPORT {
-        ext.args = "--seq_header accession --delim ' '"
+        ext.args = "--seq_header species --delim ' '"
         publishDir = [
             path: { "${params.outdir}/crabs_dbimport" },
             mode: params.publish_dir_mode

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -18,11 +18,14 @@ params {
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/samplesheet/test_samplesheet.csv'
     fasta  = 'https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/testdata/GCF_024334085.1_ASM2433408v1_genomic.fna.gz'
 
-    metagenome = true
-    metagenome_n_genomes = '1'
-    metagenome_n_reads = '100'
-    amplicon = true
-    target_capture = true
-    probe_ref_name = 'Diptera-2.7Kv1'
-    wholegenome = true
+    amplicon              = true
+    metagenome            = true
+    target_capture        = true
+    wholegenome           = true
+
+    fw_primer             = 'AAAATAAT'
+    rv_primer             = 'GATTACTTT'
+    amplicon_read_count   = 1000
+    metagenome_n_reads    = '100K'
+    probe_ref_name        = 'Diptera-2.7Kv1'
 }
diff --git a/modules/local/insilicoseq_generate.nf b/modules/local/insilicoseq_generate.nf
@@ -1,6 +1,6 @@
 process INSILICOSEQ_GENERATE {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_low'
 
     conda "bioconda::insilicoseq=1.6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -51,22 +51,22 @@
             "properties": {
                 "amplicon": {
                     "type": "boolean",
-                    "description": "Option to simulate amplicon data.",
+                    "description": "Option to simulate amplicon sequencing reads.",
                     "fa_icon": "fas fa-question-circle"
                 },
                 "target_capture": {
                     "type": "boolean",
-                    "description": "Option to simulate UCE target capture data.",
+                    "description": "Option to simulate target capture sequencing reads.",
                     "fa_icon": "fas fa-question-circle"
                 },
                 "metagenome": {
                     "type": "boolean",
-                    "description": "Option to simulate metagenomic data.",
+                    "description": "Option to simulate metagenomic sequencing reads.",
                     "fa_icon": "fas fa-question-circle"
                 },
                 "wholegenome": {
                     "type": "boolean",
-                    "description": "Option to simulate wholegenomic data.",
+                    "description": "Option to simulate wholegenomic sequencing reads.",
                     "fa_icon": "fas fa-question-circle"
                 }
             }
@@ -75,7 +75,7 @@
             "title": "Amplicon options",
             "type": "object",
             "fa_icon": "fas fa-dna",
-            "description": "Options for simulating amplicon data.",
+            "description": "Options for simulating amplicon sequencing reads.",
             "properties": {
                 "fw_primer": {
                     "type": "string",
@@ -102,7 +102,8 @@
                 "amplicon_ncbi_query": {
                     "type": "string",
                     "description": "NCBI query to use when `--amplicon_ref_source` is set to 'ncbi'",
-                    "default": "16S[All Fields] AND (\"1\"[SLEN] : \"50000\"[SLEN])"
+                    "default": "16S[All Fields] AND (\"1\"[SLEN] : \"50000\"[SLEN])",
+                    "help_text": "Multiple species can be queried like this '(\"Mus musculus\"[Organism] OR \"Salmo salar\"[Organism]) AND 16S[All Fields]'"
                 },
                 "amplicon_ncbi_batchsize": {
                     "type": "integer",
@@ -142,7 +143,7 @@
             "title": "Target capture options",
             "type": "object",
             "fa_icon": "fas fa-dna",
-            "description": "Options for simulating target capture data.",
+            "description": "Options for simulating target capture sequencing reads.",
             "properties": {
                 "target_capture_pacbio": {
                     "type": "boolean",
@@ -184,7 +185,7 @@
             "title": "Metagenome options",
             "type": "object",
             "fa_icon": "fas fa-dna",
-            "description": "Options for simulating metagenomic data.",
+            "description": "Options for simulating metagenomic sequencing reads.",
             "properties": {
                 "metagenome_ncbi_db": {
                     "type": "string",
@@ -258,7 +259,7 @@
             "title": "Wholegenome options",
             "type": "object",
             "fa_icon": "fas fa-dna",
-            "description": "Options for simulating wholegenome data.",
+            "description": "Options for simulating wholegenome sequencing reads.",
             "properties": {
                 "wholegenome_error_rate": {
                     "type": "number",
@@ -325,8 +326,8 @@
                     "exists": true,
                     "mimetype": "text/plain",
                     "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
-                    "description": "Path to FASTA genome file.",
-                    "help_text": "This parameter is *mandatory* if `--genome` is not specified, unless simulating amplicon data. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
+                    "description": "Path to reference FASTA file.",
+                    "help_text": "If this parameter is not used, the pipeline will download a fasta file, either using the `--genome` parameter or by using other parameters specific to individual modes (e.g., the `--amplicon` mode has parameters specific to just that mode.).",
                     "fa_icon": "far fa-file-code"
                 },
                 "igenomes_base": {