fixed bugs caused by merge

nf-core · Oct 30, 2024 · 40f27a5 · 40f27a5
1 parent e639e7d
commit 40f27a5
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Showing 30 changed files with 291 additions and 402 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -9,7 +9,7 @@ template:
   description: Surveillance of plant pathogens using high-throughput sequencing
   force: false
   is_nfcore: true
-  name: plantpathsurveil
+  name: pathogensurveillance
   org: nf-core
   outdir: .
   skip_features: null

diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -1,33 +1,65 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/plantpathsurveil/master/assets/schema_input.json",
-    "title": "nf-core/plantpathsurveil pipeline - params.input schema",
-    "description": "Schema for the file provided with params.input",
+    "$id": "https://raw.githubusercontent.com/nf-core/pathogensurveillance/master/assets/schema_input.json",
+    "title": "nf-core/pathogensurveillance pipeline - params.sample_data schema",
+    "description": "Schema for the file provided with params.sample_data",
     "type": "array",
     "items": {
         "type": "object",
         "properties": {
-            "sample": {
-                "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces",
-                "meta": ["id"]
+            "sample_id": {
+                "type": "string"
+            },
+            "name": {
+                "type": "string"
             },
-            "fastq_1": {
+            "description": {
+                "type": "string"
+            },
+            "path": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
-            "fastq_2": {
+            "path_2": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
-            }
+            },
+            "ncbi_accession": {
+                "type": "string",
+                "pattern": "^[A-Z]{3}[0-9]+$",
+                "errorMessage": "The `ncbi_accession` column contains at least on value that does not look like an NCBI accession (3 captial letters followed by numbers)."
+            },
+            "ncbi_query": {
+                "type": "string"
+            },
+            "ncbi_query_max": {
+                "type": "string"
+            },
+            "sequence_type": {
+                "type": "string"
+            },
+            "report_group_ids": {
+                "type": "string"
+            },
+            "color_by": {
+                "type": "string"
+            },
+            "ploidy": {
+                "type": "number"
+            },
+            "enabled": {
+                "type": "boolean"
+            },
+            "ref_group_ids": {
+                "type": "string"
+            },
         },
-        "required": ["sample", "fastq_1"]
+        "required": []
     }
 }
diff --git a/conf/aps_workshop.config b/conf/aps_workshop.config
@@ -16,7 +16,7 @@ params {
 
     // Input data
     sample_data  = 'test/data/metadata/aps_workshop.csv'
-    out_dir = 'aps_workshop_output'
+    outdir = 'aps_workshop_output'
     download_bakta_db = true
     cache_type = 'lenient'
 }
diff --git a/conf/base.config b/conf/base.config
@@ -62,19 +62,19 @@ process {
 
 report {
     enabled   = true
-    file      = "${params.out_dir}/pipeline_info/execution_report.html"
+    file      = "${params.outdir}/pipeline_info/execution_report.html"
     overwrite = true
 }
 
 timeline {
     enabled   = true
-    file      = "${params.out_dir}/pipeline_info/timeline_report.html"
+    file      = "${params.outdir}/pipeline_info/timeline_report.html"
     overwrite = true
 }
 
 trace {
     enabled   = true
-    file      = "${params.out_dir}/pipeline_info/trace_report.tsv"
+    file      = "${params.outdir}/pipeline_info/trace_report.tsv"
     overwrite = true
     fields    = "task_id,hash,native_id,process,tag,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes,vol_ctxt,inv_ctxt,workdir,scratch,error_action"
 }

diff --git a/conf/chaos.config b/conf/chaos.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-core/pathogensurveillance -profile xanthomonas,<docker/singularity> --out_dir <OUTDIR>
+        nextflow run nf-core/pathogensurveillance -profile xanthomonas,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -17,7 +17,7 @@ params {
     // Input data
     sample_data = 'test/data/metadata/chaos_samples.csv'
     reference_data = 'test/data/metadata/chaos_references.csv'
-    out_dir = 'test/output/chaos'
+    outdir = 'test/output/chaos'
     download_bakta_db = true
 }
 
diff --git a/conf/complex.config b/conf/complex.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-core/pathogensurveillance -profile xanthomonas,<docker/singularity> --out_dir <OUTDIR>
+        nextflow run nf-core/pathogensurveillance -profile xanthomonas,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -16,7 +16,7 @@ params {
 
     // Input data
     sample_data = 'test/data/metadata/complex.csv'
-    out_dir = 'test/output/complex'
+    outdir = 'test/output/complex'
     download_bakta_db = true
 }
 
diff --git a/conf/complex_minimal.config b/conf/complex_minimal.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-core/pathogensurveillance -profile xanthomonas,<docker/singularity> --out_dir <OUTDIR>
+        nextflow run nf-core/pathogensurveillance -profile xanthomonas,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -16,7 +16,7 @@ params {
 
     // Input data
     sample_data = 'test/data/metadata/complex_minimal.csv'
-    out_dir = 'test/output/complex_minimal'
+    outdir = 'test/output/complex_minimal'
     download_bakta_db = true
 }
 
diff --git a/conf/complex_small.config b/conf/complex_small.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-core/pathogensurveillance -profile xanthomonas,<docker/singularity> --out_dir <OUTDIR>
+        nextflow run nf-core/pathogensurveillance -profile xanthomonas,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -16,7 +16,7 @@ params {
 
     // Input data
     sample_data = 'test/data/metadata/complex_small.csv'
-    out_dir = 'test/output/complex_small'
+    outdir = 'test/output/complex_small'
     download_bakta_db = true
 }
 
diff --git a/conf/fungi_n81.config b/conf/fungi_n81.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/plantpathsurveil -profile fungi_n81,<docker/singularity> --out_dir <OUTDIR>
+        nextflow run nf-core/plantpathsurveil -profile fungi_n81,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -15,6 +15,6 @@ params {
 
     // Input data
     sample_data = 'test/data/metadata/boxwood.csv'
-    out_dir = 'test/output/fungi_n81'
+    outdir = 'test/output/fungi_n81'
     download_bakta_db = false
 }
diff --git a/conf/high_complexity_kpneumoniae.config b/conf/high_complexity_kpneumoniae.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/plantpathsurveil -profile high_complexity_kpneumoniae,<docker/singularity> --out_dir <OUTDIR>
+        nextflow run nf-core/plantpathsurveil -profile high_complexity_kpneumoniae,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -15,7 +15,7 @@ params {
 
     // Input data
     sample_data = 'test/data/metadata/high_complexity_kpneumoniae.csv'
-    out_dir = 'test/output/high_complexity_kpneumoniae'
+    outdir = 'test/output/high_complexity_kpneumoniae'
     download_bakta_db = true
 }
 

diff --git a/conf/mixed.config b/conf/mixed.config
@@ -5,6 +5,6 @@ params {
     // Input data
     sample_data = 'test/data/metadata/mixed.csv'
     reference_data = 'test/data/metadata/mixed_references.csv'
-    out_dir = 'test/output/mixed'
+    outdir = 'test/output/mixed'
     download_bakta_db = true
 }
diff --git a/conf/mixed_bacteria.config b/conf/mixed_bacteria.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/plantpathsurveil -profile mixed_bacteria,<docker/singularity> --out_dir <OUTDIR>
+        nextflow run nf-core/plantpathsurveil -profile mixed_bacteria,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -15,6 +15,6 @@ params {
 
     // Input data
     sample_data = 'test/data/metadata/mixed_bacteria.csv'
-    out_dir = 'test/output/mixed_bacteria'
+    outdir = 'test/output/mixed_bacteria'
     download_bakta_db = true
 }