fix: align qc container (#928)

* revert csvkit to align_qc container * update changelog * add PR no. to changelog
Clinical-Genomics · May 4, 2022 · 904d183 · 904d183
1 parent 1b5008f
commit 904d183
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diff --git a/BALSAMIC/config/balsamic_env.yaml b/BALSAMIC/config/balsamic_env.yaml
@@ -6,6 +6,7 @@ align_qc:
   - picard
   - multiqc
   - fastp
+  - csvkit
 annotate:
   - ensembl-vep
   - vcfanno

diff --git a/BALSAMIC/constants/common.py b/BALSAMIC/constants/common.py
@@ -63,6 +63,7 @@
     "picard": "align_qc",
     "multiqc": "align_qc",
     "fastp": "align_qc",
+    "csvkit": "align_qc",
     "ensembl-vep": "annotate",
     "genmod": "annotate",
     "vcfanno": "annotate",

diff --git a/BALSAMIC/containers/align_qc/align_qc.yaml b/BALSAMIC/containers/align_qc/align_qc.yaml
@@ -10,4 +10,7 @@ dependencies:
   - bioconda::picard=2.27.1
   - bioconda::multiqc=1.12
   - bioconda::fastp=0.23.2
+  - conda-forge::csvkit=1.0.7
+  - conda-forge::libiconv=1.16
+  - conda-forge::fontconfig=2.14.0
   - conda-forge::r-base=4.1.3
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,3 +1,10 @@
+[9.0.1]
+-------
+
+Fixed:
+^^^^^^
+* Revert `csvkit` tool in align_qc container #928 
+
 [9.0.0]
 --------
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,6 +6,7 @@ align_qc: @@
       - picard
       - multiqc
       - fastp
+      - csvkit
     annotate:
       - ensembl-vep
       - vcfanno
@@ Expand Down @@