#NOW:
#
# - you will have records of what was done in the sample directories (see err
#   and logfiles/*).
#
# - having run the xsummarize_alignments script should have created the
#   tab-delimited file ProcessingAndAlignmentResults.tsv, which summarizes
#   the numbers of reads and alignments at the various stages of processing,
#   from initial input to final alignments used for the next workflow step
#
# - you should find in this directory bamfiles.tsv, which tabulates the samples
#   and location of the generated *.bam alignment files. bamfiles.tsv can be
#   used as input to TSRchitect for the next workflow step: identification of
#   TSS and TSR; see directory tsr and instructions tsr/0Record.
#
(echo "... changing into directory 'tsr' and executing 'xrunwfSc all' with"; \
 echo "    a TSRchitect singularity image ..."; \
	cd tsr && \
	singularity pull -F --name tsr.simg shub://BrendelGroup/TSRchitect && \
 	singularity exec -e -B ../ tsr.simg ./xrunwfSc all; \
echo "... all done; please see tsr/0Record for more ways to explore the"; \
echo "    output data"\
)
