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  • Marius
    started a topic Problem using BASH to pipe Piccard command

    Problem using BASH to pipe Piccard command

    I'm new to Bash, but would like to use it.
    I would like to pipe two Picard (GATK pipeline) commands using Bash. Each of these commands works fine when they are run as individual Bash scripts (see below). However, when I try to combine them within a single bash script, it no longer works. I really cannot find the bug though. Help is much appreciated.


    BASH Script 1
    #!/bin/bash

    # Set paths
    picardtools='PATH/picard.jar'
    bams="PATH/BAM"
    outSorted='PATH/outSorted'

    for i in BamFile1 BamFile2
    do
    java -jar $picardtools SortSam INPUT=$bams/"$i" OUTPUT=$outSorted/"$i" SORT_ORDER=coordinate CREATE_INDEX=TRUE VALIDATION_STRINGENCY=LENIENT
    done


    BASH Script 2
    #!/bin/bash

    # Set paths
    picardtools='PATH/picard.jar'
    outSorted='PATH/outSorted'
    outSorted2='PATH/outSorted2'

    for i in BamFile1 BamFile2
    do
    java -jar $picardtools AddOrReplaceReadGroups INPUT=$outSorted/$i OUTPUT=$outSorted2/"$i" SORT_ORDER=coordinate RGID="$i" RGLB="$i" RGPL=illumina RGPU="$i" RGSM="$i" CREATE_INDEX=True
    done


    ######################

    Here my attempts to pipe the two Scripts into one. But neither of these attempts worked. Can you help me find out why?

    Attempt 1
    #!/bin/bash

    # Set paths
    picardtools='PATH/picard.jar'
    bams="PATH/BAM"
    outSorted='PATH/outSorted'
    outSorted2='PATH/outSorted2'

    for i in BamFile1 BamFile2
    do
    java -jar $picardtools SortSam INPUT=$bams/"$i" OUTPUT=$outSorted/"$i" SORT_ORDER=coordinate CREATE_INDEX=TRUE VALIDATION_STRINGENCY=LENIENT
    java -jar $picardtools AddOrReplaceReadGroups INPUT=$outSorted/$i OUTPUT=$outSorted2/"$i" SORT_ORDER=coordinate RGID="$i" RGLB="$i" RGPL=illumina RGPU="$i" RGSM="$i" CREATE_INDEX=True
    done


    Attempt 2
    #!/bin/bash

    # Set paths
    picardtools='PATH/picard.jar'
    bams="PATH/BAM"
    outSorted2='PATH/outSorted2'

    for i in BamFile1 BamFile2
    do
    java -jar $picardtools SortSam INPUT=$bams/"$i" OUTPUT=/dev/stdout SORT_ORDER=coordinate CREATE_INDEX=TRUE VALIDATION_STRINGENCY=LENIENT | \
    java -jar $picardtools AddOrReplaceReadGroups INPUT=/dev/stdin OUTPUT=$outSorted2/"$i" SORT_ORDER=coordinate RGID="$i" RGLB="$i" RGPL=illumina RGPU="$i" RGSM="$i" CREATE_INDEX=True
    done

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  • seqadmin
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