cleanintermediate: $(CHIPCAP_OUTPUT)
in chipcap.mk should become cleanintermediate: all
In runchipcap.mk add cleanintermediate to getCommand
getCommand = $(MAKE) -f /data/DIV5/SASC/project-064-ronald-svdz/analysis/pipelines/chipcap/chipcap.mk \
IN_DIR=/data/DIV5/SASC/project-064-ronald-svdz/input/$(1) \
OUT_DIR=/data/DIV5/SASC/project-064-ronald-svdz/analysis/runs/$(2) \
CHIPCAP_VER=0.1.2 \
FASTQ_EXT=fastq \
CHIPCAP_INPUT=$(3) \
CHIPCAP_QC_MODE=cliptrim \
GZIP_EXT=gz \
MACS14_EXE=/home/sajvanderzeeuw/.virtualenvs/ronald/bin/macs \
PYTHON_EXE=/home/sajvanderzeeuw/.virtualenvs/ronald/bin/python2.7 \
OPT_MACS14_mfold=$(4),$(5) cleanintermediate
#OPT_MACS14_control=control.bam