Merge pull request #12 from BDI-pathogens/slurm_update_errors

Add missing CONDA_BIN prefixes; identified following Slurm update
BDI-pathogens · Oct 31, 2022 · f5231b4 · f5231b4
2 parents c42bb19 + 8eca74c
commit f5231b4
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diff --git a/snakemake/auxfiles/shiver_config_raw.sh b/snakemake/auxfiles/shiver_config_raw.sh
@@ -220,7 +220,7 @@ deduplicate=true
 # include options in this command, such as a non-default
 # DUPLICATE_SCORING_STRATEGY, but do not include options relating to file-naming
 # or the associated shiver commands will break):
-DeduplicationCommand="picard MarkDuplicates"
+DeduplicationCommand="${CONDA_BIN}/picard MarkDuplicates"
 
 # Shall we remap to the consensus? (For remapping, gaps in coverage in the
 # consensus will filled in by the corresponding part of the orginal reference,

diff --git a/snakemake/scripts/qc/qc_consensus.sh b/snakemake/scripts/qc/qc_consensus.sh
@@ -138,7 +138,7 @@ get_mapped() {
 
 get_mapped_positive() {
   echo "INFO: Get mapped_positive" >>"${LOG}"
-  mapped_positive=$(($(samtools view -f3 "${IN_FILE_BAM}" | awk '($2!=147)&&($2!=99)' | wc -l) / 2))
+  mapped_positive=$(($("${CONDA_BIN}"/samtools view -f3 "${IN_FILE_BAM}" | awk '($2!=147)&&($2!=99)' | wc -l) / 2))
   echo -n "${mapped_positive}," >>"${OUT_FILE}"
   echo "DEBUG: ${mapped_positive}," >>"${LOG}"
 }