fixes after review

EBI-Metagenomics · Nov 8, 2024 · 380ad87 · 380ad87
1 parent 3948397
commit 380ad87
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Showing 7 changed files with 37 additions and 25 deletions.
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -28,7 +28,7 @@ jobs:
     - name: Install dependencies
       run: |
         pip install -r requirements-test.txt
-        pip install --upgrade numpy pandas
+        pip install --upgrade pandas==1.4.0
     - name: Unit tests
       run: |
         # TODO, improve the pythonpath handling

diff --git a/bin/parse_viral_pred.py b/bin/parse_viral_pred.py
@@ -222,14 +222,13 @@ def parse_virus_sorter2(sorter_files, vs_cutoff):
     prophages = dict()
 
     final_boundary_file, final_score_file, final_combined_fa_file = "", "", ""
-    print('SORTER',sorter_files)
-    for i in sorter_files:
-        if "final-viral-boundary.tsv" in i:
-            final_boundary_file = i
-        elif "final-viral-score.tsv" in i:
-            final_score_file = i
-        elif "final-viral-combined.fa" in i:
-            final_combined_fa_file = i
+    for sorter_results_file in sorter_files:
+        if "final-viral-boundary.tsv" in sorter_results_file:
+            final_boundary_file = sorter_results_file
+        elif "final-viral-score.tsv" in sorter_results_file:
+            final_score_file = sorter_results_file
+        elif "final-viral-combined.fa" in sorter_results_file:
+            final_combined_fa_file = sorter_results_file
         else:
             print('ERROR: The result files of VirSorter2 are incomplete. The code expects the files final-viral-{boundary,score}.tsv and final-viral-combined.fa.', file=sys.stderr)
             return high_confidence, low_confidence, prophages

diff --git a/modules/local/utils.nf b/modules/local/utils.nf
@@ -1,4 +1,4 @@
-process CONCATENATE_FILES {
+process CONCATENATE_VIRSORTER2_FILES {
     tag "${meta.id}"
     label "process_medium"
 
@@ -15,6 +15,5 @@ process CONCATENATE_FILES {
     grep 'seqname' inputs/\${first_file} > header.tsv || true
     cat inputs/* | grep -v 'seqname' > without_header.${output_name}
     cat header.tsv without_header.${output_name} > ${output_name}
-    rm without_header.${output_name}
     """
 }
diff --git a/modules/local/virsorter2/main.nf b/modules/local/virsorter2/main.nf
@@ -4,11 +4,11 @@ process VIRSORTER2 {
     container 'quay.io/microbiome-informatics/virsorter:2.2.4'
 
     input:
-      tuple val(meta), file(fasta), val(contig_number) 
+      tuple val(meta), file(fasta), val(number_of_contigs) 
       path(database) 
 
     when: 
-      contig_number.toInteger() > 0 
+      number_of_contigs.toInteger() > 0 
 
     output:
       tuple val(meta), path("*.final-viral-score.tsv"),    emit: score_tsv
@@ -18,7 +18,8 @@ process VIRSORTER2 {
     script:
       def args = task.ext.args ?: ''
       """
-      # speed up hmmsearch
+      # Settings to speed up hmmsearch
+      # TODO: this needs to be tested, it doesn't seem to speed up so we decided to chunk the fasta instead
       #virsorter config --set HMMSEARCH_THREADS=4
       #virsorter config --set FAA_BP_PER_SPLIT=50000
       

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -72,6 +72,7 @@
                 },
                 "output": {
                     "type": "string",
+                    "format": "directory-path",
                     "default": "results",
                     "description": "name of the result folder"
                 }
@@ -85,10 +86,12 @@
             "properties": {
                 "virsorter": {
                     "type": "string",
+                    "format": "directory-path",
                     "description": "a virsorter database provided as 'virsorter/virsorter-data'"
                 },
                 "virsorter2": {
                     "type": "string",
+                    "format": "directory-path",
                     "description": "a virsorter2 database"
                 },
                 "virfinder": {
@@ -243,52 +246,62 @@
             "properties": {
                 "assemblydir": {
                     "type": "string",
+                    "format": "directory-path",
                     "default": "00-assembly",
                     "description": "output directory for assembly step",
                     "fa_icon": "far fa-file-code"
                 },
                 "virusdir": {
                     "type": "string",
+                    "format": "directory-path",
                     "default": "01-viruses",
                     "description": "output directory for detected viruses step"
                 },
                 "prodigaldir": {
                     "type": "string",
+                    "format": "directory-path",
                     "default": "02-prodigal",
                     "description": "output directory for prodigal step"
                 },
                 "phanotatedir": {
                     "type": "string",
+                    "format": "directory-path",
                     "default": "02-phanotate",
                     "description": "output directory for phanotate step"
                 },
                 "hmmerdir": {
                     "type": "string",
+                    "format": "directory-path",
                     "default": "03-hmmer",
                     "description": "output directory for hmmer step"
                 },
                 "blastdir": {
                     "type": "string",
+                    "format": "directory-path",
                     "default": "04-blast",
                     "description": "output directory for blast step"
                 },
                 "plotdir": {
                     "type": "string",
+                    "format": "directory-path",
                     "default": "05-plots",
                     "description": "output directory for plots"
                 },
                 "taxdir": {
                     "type": "string",
+                    "format": "directory-path",
                     "default": "06-taxonomy",
                     "description": "output directory for taxonomy results"
                 },
                 "checkvdir": {
                     "type": "string",
+                    "format": "directory-path",
                     "default": "07-checkv",
                     "description": "output directory for checkV step"
                 },
                 "finaldir": {
                     "type": "string",
+                    "format": "directory-path",
                     "default": "08-final",
                     "description": "final output directory"
                 }

diff --git a/subworkflows/local/detect.nf b/subworkflows/local/detect.nf
@@ -2,14 +2,14 @@
  * Run virus detection tools and parse the predictions according to defined filters. 
 */
 
-include { VIRSORTER                                       } from '../../modules/local/virsorter' 
-include { VIRSORTER2                                      } from '../../modules/local/virsorter2' 
-include { VIRFINDER                                       } from '../../modules/local/virfinder' 
-include { PPRMETA                                         } from '../../modules/local/pprmeta'
-include { PARSE                                           } from '../../modules/local/parse'
-include { CONCATENATE_FILES as CONCATENATE_FILES_SCORE    } from '../../modules/local/utils'
-include { CONCATENATE_FILES as CONCATENATE_FILES_BOUNDARY } from '../../modules/local/utils'
-include { CONCATENATE_FILES as CONCATENATE_FILES_FA       } from '../../modules/local/utils'
+include { VIRSORTER                                                  } from '../../modules/local/virsorter' 
+include { VIRSORTER2                                                 } from '../../modules/local/virsorter2' 
+include { VIRFINDER                                                  } from '../../modules/local/virfinder' 
+include { PPRMETA                                                    } from '../../modules/local/pprmeta'
+include { PARSE                                                      } from '../../modules/local/parse'
+include { CONCATENATE_VIRSORTER2_FILES as CONCATENATE_FILES_SCORE    } from '../../modules/local/utils'
+include { CONCATENATE_VIRSORTER2_FILES as CONCATENATE_FILES_BOUNDARY } from '../../modules/local/utils'
+include { CONCATENATE_VIRSORTER2_FILES as CONCATENATE_FILES_FA       } from '../../modules/local/utils'
 
 workflow DETECT {
 
@@ -38,9 +38,9 @@ workflow DETECT {
       virsorter_output = VIRSORTER.out
     }
     else {
-      // chunk fasta by 10Mb
+      // chunk fasta by 500Mb
       chunked_ch = length_filtered_ch.flatMap{ meta, fasta, value ->
-          def chunks = fasta.splitFasta(file: true, size: 10.MB);
+          def chunks = fasta.splitFasta(file: true, size: 500.MB);
           chunks.collect{ chunk ->
              return tuple(meta, chunk, value);
           }

diff --git a/tests/test_parse_viral_preds.py b/tests/test_parse_viral_preds.py
@@ -228,7 +228,7 @@ def test_virsorter_precedence(self):
         shutil.rmtree(test_dir)
 
     def test_virsorter2_precedence(self):
-        """VirSorter2 results take precedence over the other tools
+        """VirSorter2 results should take precedence over the other tools
         """
         pprmeta_path = self._build_path("/virsorter_precedence/pprmeta.csv")
         vf_path = self._build_path("/virsorter_precedence/virfinder.txt")