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Added sample tools.groovy sample + portability fixes
- avoid zcat due to OS X issue with syntax - define type for all run_salmon stages (otherwise breaks with newer bpipe versions) - remove quant type from create_salmon_index (legacy code)
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-6
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+16
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.gitignore

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@@ -1,4 +1,4 @@
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tools*
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tools/*
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ref*
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*/__pycache__
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allvars-case*

MINTIE.groovy

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@@ -92,7 +92,7 @@ assemble = {
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""", "assemble"
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} else {
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exec """
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rlens=`zcat $input1 $input2 \
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rlens=`gunzip -c $input1 $input2 \
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| awk -v mrl=$min_read_length 'BEGIN {minlen = mrl; maxlen = 0} {
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if (NR % 4 == 2) {
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rlen = length(\$1) ;
@@ -138,9 +138,6 @@ assemble = {
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create_salmon_index = {
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def sample_name = branch.name
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def salmon_index = sample_name + "/all_fasta_index"
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if (type == "quant") {
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salmon_index = sample_name + "/salmon_quant_index"
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}
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output.dir = salmon_index
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def index_fasta = output.dir + "/" + sample_name + ".fasta"
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produce(index_fasta, '*.bin'){
@@ -307,7 +304,7 @@ run { fastqCaseFormat * [ fastq_dedupe +
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trim +
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assemble +
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create_salmon_index +
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[ fastqCaseFormat * [ run_salmon ],
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[ fastqCaseFormat * [ run_salmon.using(type: "case") ],
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fastqControlFormat * [ run_salmon.using(type:"controls") ] ] +
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create_ec_count_matrix +
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run_de +

tools.groovy

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// Path to tools used by the MINTIE pipeline
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bpipe="bpipe"
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fastuniq="fastuniq"
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dedupe="dedupe.sh"
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trimmomatic="trimmomatic"
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fasta_formatter="fasta_formatter"
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samtools="samtools"
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bedtools="bedtools"
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soapdenovotrans="SOAPdenovo-Trans-127mer"
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salmon="salmon"
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gmap="gmap"
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R="R"
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python="python"

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