update conda channels in envs/MetaSnk.yaml

sole issue with reading paths for RAW_DIR and OUT_DIR in configuration file. Avoids using PWD and asks for always providing absolute paths

Update MetaSnk.yaml, no includes specifics channels where to look for dependencies. Fixes error due to unsolved environment when looking for snakemake.

correct bug when setting connfiguration with --configfile at execution, and allow use of environmental variable PWD in config.yaml

add rule get_human_ref to automatically download human reference and place it in the METASNK_DBS directory

replace rule strphlan_check with strphlan_summary to agregate info files from StrainPhlAn into a report table

include removal of columns with zero values in rule metaphlan2_merge, flag output files as reports and add rst files with reports descriptions

update PhlAnProf rules, add lines of code to strphlan_clade_profiling to create additional figures with ggtree

add module PhlAnProf, and update existing rules, READMEs accordingly. Also add rules to pull singularity containers and to download reference data

add rule summarize_raw to rules/rawQC.smk, this rule creates summarizing tables and figures that are included in the snakemake html report (snakemake rawQC --report rawQC.html)

rename rule multiqc_raw_listing_files, set message for rule fastqc_raw and change directory to store ourput of rule multiqc_raw_list_files

edit multiqc_raw to force overwritting existing multiqc reports AND remove line in fastqc_raw that created non-needed directory