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Verified Commit bf23c27b authored by Mia Croiset's avatar Mia Croiset
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add the pairtools command to output final pairs file

parent ea672538
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......@@ -11,6 +11,7 @@ process BUILD_MATRIX {
output:
tuple val(meta), path("${meta1.id}_*"), emit: matrix
path "*.log", emit: log_file
path "*.gz", emit: final_pairs
script:
......@@ -21,6 +22,8 @@ process BUILD_MATRIX {
grep -v ^# ${idx_pairs} | sort -S 2G -k8,8n -k9,9n --parallel=1 >> ${args}.pre.pairs
hicstuff_build_matrix.py -p ${args}.pre.pairs -f ${fragments_list} -t graal -o ${args}
pairtools sort ${idx_pairs} --output ${idx_pairs}.gz --c1 chr1 --c2 chr2 --p1 pos1 --p2 pos2 --pt frag1
mv ${args} ${meta1.id}_${args}
mv hicstuff_matrix.log hicstuff_${meta1.id}_matrix_sparse.log
"""
......
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