Bug fixes

bin/csv_adorn.py

@@ -12,8 +12,13 @@ def csv_adorn(path: str, header: str) -> None:
     """
     print(f"id,{header}")
     with open(path) as f:
+        any_data = False
         for line in f:
+            any_data = True
             print(line.strip() + ",1")
+        if not any_data:
+            # this is a stupid hack, but the only way we found that does not break modularity
+            print("nothing,0")
 
 
 def main() -> None:

bin/make_score_table.py

@@ -48,6 +48,9 @@ def main() -> None:
 
     # Print the data
     for i, row in enumerate(data):
+        # this if cleans up the stupid hack from csv_adorn
+        if scores[i] == 0:
+            continue
         print(row[0] + "," + id_formats[i] + "," + ",".join(row[1:]) + "," + str(scores[i]))
 
 

bin/make_stats.py

@@ -24,11 +24,11 @@ def make_stats(score_table: str) -> None:
 
     # calculate stats
     n = len(scores)
-    mode = max(set(scores), key=scores.count)
-    mean = sum(scores) / n
+    mode = max(set(scores), key=scores.count) if scores else 0
+    mean = sum(scores) / n if n else 0
     goodness = mean / max_score
-    percent_max = sum(score == max_score for score in scores) / n
-    percent_privates = sum(score == 1 for score in scores) / n
+    percent_max = sum(score == max_score for score in scores) / n if n else 0
+    percent_privates = sum(score == 1 for score in scores) / n if n else 0
 
     # print stats as yaml
     print(f"n: {n}")

bin/plot_orthologs.R

@@ -49,6 +49,10 @@ empty_plots <- function(e) {
 }
 data <- tryCatch(read.csv(args[1], header = TRUE, stringsAsFactors = FALSE), error = empty_plots)
 
+if (nrow(data) == 0) {
+    empty_plots()
+}
+
 # Melt the data keeping ID and score
 melted_data <- melt(data, id.vars = c("id", "id_format", "score"), variable.name = "method", value.name = "support") %>%
     filter(support == 1) %>%

bin/score_hits.py

@@ -41,7 +41,7 @@ def filter_centroid(data) -> list:
         if sum([column[i] for column in columns]) > 1:
             for j in range(len(columns[i])):
                 scores[i] += columns[i][j]
-    ratios = [scores[i] / sum(columns[i]) for i in range(len(columns))]
+    ratios = [scores[i] / sum(columns[i]) if sum(columns[i]) else 0 for i in range(len(columns))]
 
     # get index of highest ratio
     centroid = ratios.index(max(ratios))

conf/modules.config

@@ -114,7 +114,7 @@ process {
     }
 
     withName: 'MERGE_HITS' {
-        ext.args = "-u NA"
+        ext.args = "-u 0 -k"
         ext.prefix = "aggregated_hits"
         publishDir = [
             path: { "${params.outdir}/orthologs/hits" },

modules/local/fetch_eggnog_group_local.nf

@@ -2,11 +2,6 @@ process FETCH_EGGNOG_GROUP_LOCAL {
     tag "$meta.id"
     label 'process_single'
 
-    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
-        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
-
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :

modules/local/fetch_oma_group_local.nf

@@ -2,11 +2,6 @@ process FETCH_OMA_GROUP_LOCAL {
     tag "$meta.id"
     label 'process_single'
 
-    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
-        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
-
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :

modules/local/fetch_panther_group_local.nf

@@ -2,11 +2,6 @@ process FETCH_PANTHER_GROUP_LOCAL {
     tag "$meta.id"
     label 'process_single'
 
-    conda "conda-forge::python=3.10.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.10' :
-        'biocontainers/python:3.10' }"
-
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :

modules/local/filter_fasta.nf

@@ -2,11 +2,6 @@ process FILTER_FASTA {
     tag "$meta.id"
     label 'process_single'
 
-    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
-        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
-
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :