cp cellrangermulti to cellrangermulti_vdj in SCRNASEQ workflow

cp align_cellrangermulti to align_cellrangermulti_vdj in local subwor… …

…kflows

separate processes that generate reference files from cellranger multi

installed nf-core/module bamtofastq10x

add null/ to the gitignore list

add description of demultiplexing combined with immuneprofiling

add bamtofastq10x module with amendments

move reference creation outside the cellranger multi to avoid rerunni… …

…ng. additionally changing input channels

add subworkflow specific for handling sample demultiplexing followed … …

…by immune profiling

implement cellranger multi ref and vdj. branch channels to either run… …

… cellranger multi or cellranger multi+vdj

update publishDir for the two cellranger multi outputs. add publishDi… …

…r to bamtofastq process

add func to expand feature channels to match demultiplexed gex. modif… …

…ied extract_gex_fq

remove renaming of files

removed arg for BAMTOFASTQ and updated CELLRANGER_MULTI with regex

changed faux channels to value channels to be consumed infinitely and… …

… updated extract_gex_fq()

remove unused code

renamed file

update output path for fastq

update output dir for emptydrops analysis

update filename for generating reference files for cellranger multi

remove frna option for immune-profiling

updated bamtofastq10x module

update changelog and output docs

add separate test for cellranger multi when we have multiplexed sampl… …

…es which require immune profiling

update element to do cross product on when expanding channels for mul… …

…tiplexed samples

update the sorting mechanism for fq files in cellranger_multi.py

added printout of fastqs list

move expanded sorting mechanism of fq files to channel manipulation i… …

…nstead of inside cellranger_multi.py

update sorting mechanism of bam2fq outputs - fstq_dr is not an integer

update the regex search term for sorting bamtofastq output files