redirects to log file

workflow/rules/covviz.smk

@@ -9,11 +9,10 @@ rule covviz:
         "Running covviz. Project: {wildcards.project}"
     conda:
         str(WORKFLOW_PATH / "configs/env/covviz.yaml")
-    # params:
-    #     outdir = lambda wildcards, output: Path(output[0]).parent,
     shell:
         r"""
         covviz \
             --output {output} \
-            {input}
+            {input} \
+            2>&1 {log}
         """

workflow/rules/indexcov.smk

@@ -21,5 +21,6 @@ rule indexcov:
 
         {input.goleft_tool} indexcov \
             --directory {params.outdir} \
-            {params.project_dir}/[LU][WD]*/bam/*.bam
+            {params.project_dir}/[LU][WD]*/bam/*.bam \
+            2>&1 {log}
         """

workflow/rules/somalier.smk

@@ -19,7 +19,8 @@ rule extract:
             --sites {input.sites} \
             --fasta {input.ref_genome} \
             --out-dir {params.outdir} \
-            {input.bam}
+            {input.bam} \
+            2>&1 {log}
         """
 
 
@@ -47,7 +48,8 @@ rule relate:
             --ped {input.ped} \
             --infer \
             --output-prefix {params.outdir}/somalier \
-            {params.indir}/*.somalier
+            {params.indir}/*.somalier \
+            2>&1 {log}
         """
 
 
@@ -76,5 +78,6 @@ rule ancestry:
             --output-prefix {params.outdir}/somalier \
             --labels {input.labels_1kg} \
             {input.somalier_1kg}*.somalier ++ \
-            {params.indir}/*.somalier
+            {params.indir}/*.somalier \
+            2>&1 {log}
         """