cmds

nextflow run main.nf --slide $HIMC/visium_slides/V13M13-279.svs --outdir output/V13M13-279
nextflow run main_nosplit.nf --jpeg $HIMC/visium_slides/OAAEJP_OCTIY5_annotated.jpg --outdir nextflow_segmentation

cat tmp | tail -n+2 | parallel --dryrun -j1 -k --colsep '\t' "bsub_premium {1} 'nextflow run main_nosplit.nf --jpeg $HIMC/visium_slides/{1} --outdir $HIMC/himc-project-data/SAGN24/data/10X/{2}/nextflow_segmentation'"
# make directory for qupath script
cat tmp | tail -n+2 | parallel -j1 -k --colsep '\t' --dryrun "cd $HIMC/himc-project-data/SAGN24/data/10X/{2}/; mkdir -vp spatial_tmp; cp -f nextflow_segmentation/*/output/outs/* spatial_tmp/"

# Cytassit test
nextflow run main_cytassist.nf -c nextflow_cytassist.config

# Cytassist MAGA03
tail -n+2 MAGA03_input.csv | \
head -n1 | \
parallel --dryrun -j1 -k --colsep ',' \
'
bsub_premium {1/} \
"
nextflow run main_cytassist.nf \
-c nextflow_cytassist.config \
--microscopy_slide {1} \
--visium_slide {2} \
--outdir {3}
"
'

# Cytassist No downsample
nextflow run main_cytassist_nods.nf -c nextflow_cytassist.config

# Cytassist MAGA03
tail -n+2 MAGA03_input_nods.csv | \
grep -f rerun | \
parallel --dryrun -j1 -k --colsep ',' \
'
bsub_premium {1/} \
"
nextflow run main_cytassist_nods.nf \
-c nextflow_cytassist.config \
--microscopy_slide {2} \
--visium_slide {4} \
--jpeg {3} \
--alignment {5} \
--outdir {1}/segmentation \
-resume
"
'

# Cytassist MAGA03
tail -n+2 batch_cmds/MAGA03_input_20231214_nods.csv | \
parallel --dryrun -j1 -k --colsep ',' \
'
bsub_premium {1/} \
"
nextflow run main_cytassist_nods.nf \
-c nextflow_cytassist.config \
--microscopy_slide {1} \
--visium_slide {2} \
--jpeg {4} \
--alignment {5} \
--outdir {3}/segmentation \
--downsample_factor {6} \
-resume
"
'

# for FF or FFPE with microscropy slides that dont have to be split..
nextflow run main_nosplit_ds_microscopy.nf -c nextflow_cytassist.config