Include pairtools protocol

[nservant]

Description of feature

Add a new paramater --processing hicpro or --processing pairtools

propose an alternative to HiC-Pro with the analysis protocol proposed by 'dovotail' and based on bwa-mem2 and pairtools with the following steps :

• Mapping with bwa-mem (version 2 instead of 1)
• pairtools parse - get valid ligation product / parameters --min_mapq
• pairtools sort - sorting pairs
• paritools merge - merge pairs
• pairtools dedup - remove PCR dups / parameters --keep_dups
• pairtools split - generate pairs files (and final bam if useful ?)
• pairtools select - filter pairs
• pairtools stats - generate final stats

To validate ;

• Remove multi-hits - parameter --keep_multi ?
• Compatibility of pairtools with --digestion, --restriction_site, --ligation_site, --chromosome_size, --restriction_fragments parameters ?
• Filtering on fragment size with pairtools ? options --max_insert_size --min_insert_size --max_restriction_fragment_size --min_fragment_size
• Mode --dnase with pairtools ?
• Filtering based on the distance (--min_cis_dist) for --dnase mode with --pairtools

Other ideas:

• Replace --dnase option by --no_digestion for DNAseq, microC, etc.

[nservant]

First test version available with --processing pairtools

[nservant]

The options --keep_multi / --min_mapq / --min_cis_dist / --save_interaction_bam have been managed

[nservant]

First version tested.

To further validate before release ... still need to find a way to use the options :

• --min_insert_size / --max_insertisize
• --min_restriction_fragment_size / --max_restriction_fragment_size

       ext.args = { [
            "(mapq1>${params.min_mapq} and mapq2>${params.min_mapq})",
            params.min_cis_dist > 0 ? " and (abs(pos1-pos2) < ${params.min_cis_dist})" : '',
            params.keep_multi ? " and ((pair_type=='UU') or (pair_type=='UR') or (pair_type=='RU') or (pair_type=='MM') or (pair_type=='MU'))" : 
                                " and ((pair_type=='UU') or (pair_type=='UR') or (pair_type=='RU'))",
            params.dnase ? '' : " and (abs(int(rfrag1) - int(rfrag2)) > 1)",
            //params.min_insert_size > 0 ?  " and ( (rfrag_end1 - r1pos) + (rfrag_end2 - r2pos)) > ${params.min_insert_size}" : '',
            //params.max_insert_size > 0 ? " and ( (rfrag_end1 - r1pos) + (rfrag_end2 - r2pos)) < ${params.max_insert_size}" : '',
            //params.min_restriction_fragment_size > 0 ? " -t ${params.min_restriction_fragment_size}" : '',
            //params.max_restriction_fragment_size > 0 ? " -m ${params.max_restriction_fragment_size}" : '',
        ].join(' ').trim() }