fix: added arguments for fragment size mean and sd required for the salmon...

fix: added arguments for fragment size mean and sd required for the salmon quantification approach in single-end mode

.gitignore

@@ -328,6 +328,7 @@ pip-selfcheck.json
 .DS_Store
 runs/.*
 !runs/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE
+._*
 ._.DS_Store
 .snakemake/
 logs/

.gitlab-ci.yml

@@ -12,8 +12,8 @@ test:
     # add code quality tests here
     # add unit tests here
     # add script tests here
-    #- bash tests/test_scripts_labkey_to_snakemake_table/test.sh
-    #- bash tests/test_scripts_labkey_to_snakemake_api/test.sh
+    # - bash tests/test_scripts_labkey_to_snakemake_table/test.sh
+    # - bash tests/test_scripts_labkey_to_snakemake_api/test.sh
     - bash tests/test_alfa/test.sh
     # add integration tests here
     - bash tests/test_create_dag_image/test.sh

workflow/rules/single_end.snakefile.smk

@@ -237,7 +237,11 @@ rule quantification_salmon:
             "{sample}",
             "{sample}.salmon.se"),
         libType = lambda wildcards:
-                samples_table.loc[wildcards.sample, "libtype"]
+            samples_table.loc[wildcards.sample, "libtype"],
+        fraglen = lambda wildcards:
+            samples_table.loc[wildcards.sample, 'mean'],
+        fragsd = lambda wildcards:
+            samples_table.loc[wildcards.sample, 'sd']
 
     log:
         stderr = os.path.join(
@@ -262,6 +266,8 @@ rule quantification_salmon:
         --seqBias \
         --validateMappings \
         --threads {threads} \
+        --fldMean {params.fraglen} \
+        --fldSD {params.fragsd} \
         --writeUnmappedNames \
         --index {input.index} \
         --geneMap {input.gtf} \