add logs for concat gvcf and normalise

docs/examples.md

@@ -69,7 +69,7 @@ Now that we've created our sample sheet, we need to edit the config file we copi
 
 In our example we are using all of the default options. This will configure snpArcher to perform variant calling using GATK with the scatter-by-intervals approach. Also, we have set our reference genome name and path since we want to use the same genome for all samples in our sample sheet.
 
-```{yaml}
+```
 samples: "config/samples.csv" # path to the sample metadata CSV
 final_prefix: "" # prefix for final output files
 intervals: True #Set to True if you want to perform variant calling using interval approach.

docs/executing.md

@@ -47,8 +47,8 @@ Snakemake [supports most cluster schedulers](https://snakemake.github.io/snakema
 #### Install plugin
 To execute snpArcher on a SLURM cluster, you will need to install the [SLURM executor plugin](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html) into the snpArcher environment.
 ```shell
-conda activate snpArcher
-pip install pip install snakemake-executor-plugin-slurm
+conda activate snparcher
+pip install snakemake-executor-plugin-slurm
 ```
 #### Profile Setup
 To specify resources for the workflow to SLURM, you must use a workflow profile. We have provided a SLURM profile template (`profiles/slurm/config.yaml`) which you can modify to specify SLURM partitions, memory allocation, etc. Please refer to the [profiles setup section](./setup.md#resources) for more details. 

workflow/rules/bam2vcf_gatk_intervals.smk

@@ -53,8 +53,8 @@ rule concat_gvcfs:
         "../envs/bcftools.yml"
     shell:
         """
-        bcftools concat -D -a -Ou {input.gvcfs} | bcftools sort -T {resources.tmpdir} -Oz -o {output.gvcf} -
-        tabix -p vcf {output.gvcf}
+        bcftools concat -D -a -Ou {input.gvcfs} 2> {log} | bcftools sort -T {resources.tmpdir} -Oz -o {output.gvcf} - 2>> {log}
+        tabix -p vcf {output.gvcf} 2>> {log}
         """
 
 rule bcftools_norm:
@@ -73,8 +73,8 @@ rule bcftools_norm:
         "../envs/bcftools.yml"
     shell:
         """
-        bcftools norm -m +any -Oz -o {output.gvcf} {input.gvcf}
-        tabix -p vcf {output.gvcf}
+        bcftools norm -m +any -Oz -o {output.gvcf} {input.gvcf} 2> {log}
+        tabix -p vcf {output.gvcf} 2>> {log}
         """
 
 rule create_db_mapfile: