CODEWITHSUNDEEP
snakemake
user3224522
user3224522

Reputation: 1151

How to run a bash script inside a snakemake pipeline

I would like to run a bash script inside the snakemake pipeline. But I do not know how to call the input and output of snakemake in a bash script.

snakemake:

rule xxx:
    input:
        "input.vcf"
    output:
        "output.tab"
    shell:
        """
        some_bash.sh {input} {output}
        """

bash script:

#!/bin/bash

paste <(bcftools snakemake@input[0] |\
    awk -F"\t" 'BEGIN {print "CHR\tPOS\tID\tREF\tALT\tFILTER"} \
      !/^#/ {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6}') \
    \
  <(bcftools query -f '[\t%SAMPLE=%GT]\n' snakemake@input[0] |\
    awk 'BEGIN {print "nHet"} {print gsub(/0\|1|1\|0|0\/1|1\/0/, "")}') \
    \
  <(bcftools query -f '[\t%SAMPLE=%GT]\n' snakemake@input[0] |\
    awk 'BEGIN {print "nHomAlt"} {print gsub(/1\|1|1\/1/, "")}') \
    \
  <(bcftools query -f '[\t%SAMPLE=%GT]\n' snakemake@input[0] |\
    awk 'BEGIN {print "nHomRef"} {print gsub(/0\|0|0\/0/, "")}') \
    \
  <(bcftools snakemake@input[0] | awk -F"\t" '/^#CHROM/ {split($0, header, "\t"); print "HetSamples"} \
    !/^#CHROM/ {for (i=10; i<=NF; i++) {if (gsub(/0\|1|1\|0|0\/1|1\/0/, "", $(i))==1) {printf header[i]","}; if (i==NF) {printf "\n"}}}') \
    \
  <(bcftools snakemake@input[0] | awk -F"\t" '/^#CHROM/ {split($0, header, "\t"); print "HomSamplesAlt"} \
    !/^#CHROM/ {for (i=10; i<=NF; i++) {if (gsub(/1\|1|1\/1/, "", $(i))==1) {printf header[i]","}; if (i==NF) {printf "\n"}}}') \
    \
  | sed 's/,\t/\t/g' | sed 's/,$//g' > snakemake@output[0]

Error I get:

[E::main] unrecognized command 'snakemake@input[0]'
[E::main] unrecognized command 'snakemake@input[0]'
[E::main] unrecognized command 'snakemake@input[0]'
[E::hts_open_format] [E::hts_open_format] Failed to open file "snakemake@input[0]" : No such file or directoryFailed to open file "snakemake@input[0]" : No such file or directory

Upvotes: 0

Views: 743

Answers (1)

Troy Comi
Troy Comi

Reputation: 2079

You need to get the input arguments using bash syntax, snakemake@input[0] is specifically for R scripts using a script directive.

In particular, you can replace snakemake@input[0] with $1, which gets the first argument to a bash script and snakemake@output[0] with $2, the second argugment. To be safe, wrap those with double quotes in case there are spaces in the filenames, e.g. "$1".

Upvotes: 2

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