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Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
genomic-medicine-sweden · Sep 6, 2023 · c8db934 · c8db934
1 parent 62fb1b8
commit c8db934
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Showing 5 changed files with 8 additions and 6 deletions.
diff --git a/bin/drop_filter_results.py b/bin/drop_filter_results.py
@@ -8,7 +8,8 @@
 def FilteringResults(samples: list, gene_panel: str, out_drop_ae_rds: str, out_drop_gene_name: str, out_drop_as_tsv: str):
     # Read gene panel if it has been provided
     if gene_panel != "None":
-        df_panel = pd.read_csv(gene_panel, sep="\t", skiprows=26)
+        gene_panel_header = ['chromosome', 'gene_start', 'gene_stop' 'hgnc_id', 'hgnc_symbol']
+        df_panel = pd.read_csv(gene_panel, sep="\t", names=gene_panel_header, header=None, comment='#')
 
     if out_drop_ae_rds != "None":
         rds_AE = pyreadr.read_r(out_drop_ae_rds)
@@ -18,7 +19,7 @@ def FilteringResults(samples: list, gene_panel: str, out_drop_ae_rds: str, out_d
         # Count how many events are significant per provided sample
         df_family_AE_top20 = pd.DataFrame()
 
-        for id in sample:
+        for id in samples:
             df_id = df_results_family_AE[df_results_family_AE["sampleID"] == id]
             if sum(df_id["padjust"] < 0.05) < 20:
                 df_id = df_id.sort_values(by=["pValue"]).reset_index()

diff --git a/conf/modules.config b/conf/modules.config
@@ -344,7 +344,7 @@ process {
     }
 
     withName: '.*ANALYSE_TRANSCRIPTS:DROP_FILTER_RESULTS' {
-        ext.when = {params.run_drop_ae|params.run_drop_as}
+        ext.when = {params.run_drop_ae | params.run_drop_as}
         publishDir = [
             path: { "${params.outdir}/analyse_transcripts/drop" },
             mode: params.publish_dir_mode,

diff --git a/modules/local/drop_config_runAE.nf b/modules/local/drop_config_runAE.nf
@@ -47,7 +47,7 @@ process DROP_CONFIG_RUN_AE {
     snakemake aberrantExpression --cores ${task.cpus} --rerun-triggers mtime
 
     cp output/processed_results/aberrant_expression/*/outrider/outrider/OUTRIDER_results_all.Rds .
-    cp output/processed_data/preprocess/*/gene_name_mapping_* .
+    cp output/processed_data/preprocess/*/gene_name_mapping_*.tsv .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/local/drop_config_runAS.nf b/modules/local/drop_config_runAS.nf
@@ -44,7 +44,7 @@ process DROP_CONFIG_RUN_AS {
 
     snakemake aberrantSplicing --cores ${task.cpus} --rerun-triggers mtime
 
-    cp output/html/AberrantSplicing/FRASER_results_fraser--* .
+    cp output/html/AberrantSplicing/FRASER_results_fraser--*.tsv .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/local/drop_filter_results.nf b/modules/local/drop_filter_results.nf
@@ -28,11 +28,12 @@ process DROP_FILTER_RESULTS {
 
     script:
     def ids = "${samples.id}".replace("[","").replace("]","").replace(",","")
+    def gene_panel_filter = gene_panel_clinical_filter ? "--gene_panel ${gene_panel_clinical_filer}" : ''
 
     """
     $baseDir/bin/drop_filter_results.py \\
         --sample $ids \\
-        --gene_panel ${gene_panel_clinical_filter} \\
+        $gene_panel_filer \\
         --drop_ae_rds ${out_drop_ae_rds} \\
         --out_drop_gene_name ${out_drop_gene_name} \\
         --out_drop_as_tsv ${out_drop_as_tsv}