From fb36b7dce175176f17292f5db002fd0a8c36fba7 Mon Sep 17 00:00:00 2001 From: akhanf Date: Wed, 11 Nov 2020 12:31:07 -0500 Subject: [PATCH] added job groups for cluster execution --- workflow/Snakefile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/workflow/Snakefile b/workflow/Snakefile index 25ae951..972928e 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -40,6 +40,7 @@ rule smooth: output: nii = bids(root='results',datatype='func',desc='smoothed',fwhm='{fwhm}',suffix='bold.nii.gz',**config['input_wildcards']['preproc_bold']), json = bids(root='results',datatype='func',desc='smoothed',fwhm='{fwhm}',suffix='bold.json',**config['input_wildcards']['preproc_bold']) + group: 'subj' script: 'scripts/smooth.py' @@ -61,6 +62,7 @@ rule denoise: output: nii = bids(root='results',datatype='func',desc='denoised',fwhm='{fwhm}',confounds='{confounds_idx}',suffix='bold.nii.gz',**config['input_wildcards']['preproc_bold']), json= bids(root='results',datatype='func',desc='denoised',fwhm='{fwhm}',confounds='{confounds_idx}',suffix='bold.json',**config['input_wildcards']['preproc_bold']) + group: 'subj' script: 'scripts/denoise.py' @@ -76,6 +78,7 @@ rule aroma_nonaggr: output: nii = bids(root='results',datatype='func',desc='AROMAnonaggr',fwhm='{fwhm}',suffix='bold.nii.gz',**config['input_wildcards']['preproc_bold']), container: config['singularity']['fsl'] + group: 'subj' shell: 'fsl_regfilt -i {input.nii} -f `cat {input.noiseICs}` -d {input.mixing} -o {output.nii} -m {input.mask_nii}' @@ -96,6 +99,7 @@ rule aroma_aggr: output: nii = bids(root='results',datatype='func',desc='AROMAdenoised',fwhm='{fwhm}',confounds='{confounds_idx}',suffix='bold.nii.gz',**config['input_wildcards']['preproc_bold']), json= bids(root='results',datatype='func',desc='AROMAdenoised',fwhm='{fwhm}',confounds='{confounds_idx}',suffix='bold.json',**config['input_wildcards']['preproc_bold']) + group: 'subj' script: 'scripts/denoise.py'