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Allowing to use a genome not in igenomes #63

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Allowing to use a genome not in igenomes #63

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f67a227
gz issue, non nt letters in mirbase
Jan 4, 2021
c2eecd6
removing unconventional nucleotides from mirbase
Jan 11, 2021
00a044b
Apply suggestions from code review
ewels Feb 4, 2021
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13 changes: 7 additions & 6 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -306,7 +306,7 @@ if (!params.references_parsed && !params.skip_mirdeep){
file hairpin from reference_hairpin

output:
file 'genome.fa' into fasta
//file 'genome.fa' into fasta
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file 'genome.*.ebwt' into indices_mirdeep2
file 'hairpin.fa' into hairpin
file 'mature.fa' into mature
Expand All @@ -318,11 +318,11 @@ if (!params.references_parsed && !params.skip_mirdeep){
HAIRPIN="$hairpin"
if [ \${MATURE: -3} == ".gz" ]; then
gunzip -f \$MATURE
MATURE=\${MATURE: -3}
MATURE=\${MATURE%%.gz}
fi
if [ \${HAIRPIN: -3} == ".gz" ]; then
gunzip -f \$HAIRPIN
HAIRPIN=\${HAIRPIN: -3}
HAIRPIN=\${HAIRPIN%%.gz}
fi

# Remove any special base characters from reference genome FASTA file
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the line below should be:
sed '/^[^>]/s/[^ATGCatgc]/N/g' $refgenome > genome.fa

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and update below to bowtie-build genome.fa genome

Expand Down Expand Up @@ -827,7 +827,7 @@ process mirdeep2 {
!params.skip_mirdeep

input:
file refgenome from fasta
file refgenome from reference_genome
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file reads_collapsed from mirdeep_reads_collapsed
file reads_vs_refdb from reads_vs_refdb
file mature from mature
Expand All @@ -839,15 +839,16 @@ process mirdeep2 {


script:

"""
perl -ane 's/y/N/ig;print;' $hairpin > hairpin_yn.fa

miRDeep2.pl \\
$reads_collapsed \\
$refgenome \\
$reads_vs_refdb \\
$mature \\
none \\
$hairpin \\
hairpin_yn.fa \\
-d \\
-z _${reads_collapsed.simpleName}
"""
Expand Down