Fix MD tag and also remove defaults channel from envs (#38)

BCCDC-PHL · Jan 23, 2025 · 8f67678 · 8f67678
1 parent e2924c9
commit 8f67678
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Showing 3 changed files with 2 additions and 4 deletions.
diff --git a/environments/environment.yml b/environments/environment.yml
@@ -2,7 +2,6 @@ name: alignment-variants
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python=3
   - fastp=0.23.2

diff --git a/environments/plot_coverage.yml b/environments/plot_coverage.yml
@@ -2,7 +2,6 @@ name: alignment-variants-plot-coverage
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python=3
   - seaborn=0.13.2

diff --git a/modules/alignment_variants.nf b/modules/alignment_variants.nf
@@ -112,7 +112,7 @@ process minimap2 {
     printf -- "          value: null\\n"        >> ${sample_id}_minimap2_provenance.yml
     printf -- "        - parameter: -x\\n"      >> ${sample_id}_minimap2_provenance.yml
     printf -- "          value: map-ont\\n"     >> ${sample_id}_minimap2_provenance.yml
-    printf -- "        - parameter: -MD\\n"     >> ${sample_id}_minimap2_provenance.yml
+    printf -- "        - parameter: --MD\\n"    >> ${sample_id}_minimap2_provenance.yml
     printf -- "          value: null\\n"        >> ${sample_id}_minimap2_provenance.yml
     printf -- "    - tool_name: samtools\\n"    >> ${sample_id}_minimap2_provenance.yml
     printf -- "      tool_version: \$(samtools 2>&1 | grep 'Version' | cut -d ' ' -f 2)\\n"  >> ${sample_id}_minimap2_provenance.yml
@@ -125,7 +125,7 @@ process minimap2 {
 	-t ${minimap2_threads} \
 	-ax map-ont \
 	-R "@RG\\tID:${sample_id}-ONT\\tSM:${sample_id}\\tPL:ONT" \
-	-MD \
+	--MD \
 	${ref} \
 	${reads} \
 	| samtools view -@ 2 -h -F ${samtools_view_filter_flags} \