Snakefile

# ANNO = "annotation"
# ANNO_PRE = "Homo_sapiens.GRCh38.rel80.cdna.all"
#
# ANNO_FA = "{0}/{1}.fa".format(ANNO, ANNO_PRE)
# BWT_IDX = "index/{0}".format( ANNO_PRE )
#
# #RSEM_ANNO = "{ANNO}/Homo_sapiens.GRCh38.rel80.cdna.all_rsem/ref"
#
# rule all:
#     input:
#         BWT_IDX + '.1.ebwt'
#
# rule bowtie_idx:
#     input:
#         ANNO_FA
#     output:
#         expand(BWT_IDX + '.{i}.ebwt', i = range(1, 5)),
#         expand(BWT_IDX + '.rev.{i}.ebwt', i = range(1, 3))
#     shell:
#         'bowtie-build '
#         '--offrate 1 '
#         '--seed 37 '
#         #'--ftabchars 15 ' # use about a 4GB for lookup table
#         '--ntoa '
#         '{input} ' +
#         BWT_IDX

rule all:
    input:
        'final_figures.tar.gz'

rule collate_figures:
    output:
        'final_figures.tar.gz'
    params:
        output = 'final_figures'
    threads: 10
    shell:
        'touch {params.output}'
        ' && '
        'rm -rf {params.output}'
        ' && '
        'mkdir -p {params.output}'
        ' && '
        'cp -rf geuvadis/results/final_figures/* {params.output}'
        ' && '
        'cp -rf bottomly/results/final_figures/* {params.output}'
        ' && '
        'find {params.output} -name "*.pdf" | xargs -P 10 -I$ convert $ $.png'
        ' && '
        'tar -cvvf {output} {params.output}'