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Wrangler in sif #54

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merged 12 commits into from
Jan 16, 2024
Merged

Wrangler in sif #54

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7e75ca4
added files
Jan 11, 2024
ab63703
updated yaml
charliesimkin Jan 11, 2024
63a72d1
shell script bindings set up
charliesimkin Jan 11, 2024
da0c924
got the setup working
charliesimkin Jan 11, 2024
69f4ef5
got the finish working
charliesimkin Jan 11, 2024
88ddd57
removed the snakemake bindings after new sif built
charliesimkin Jan 11, 2024
d617e0f
updated the method for entering sample sheet path
charliesimkin Jan 11, 2024
1ce5746
added check run stats
charliesimkin Jan 11, 2024
555b6e6
a readme note in check run stats
charliesimkin Jan 11, 2024
97b5dbb
fix copy params
charliesimkin Jan 11, 2024
50aed0f
fix copy params
charliesimkin Jan 11, 2024
ddec564
updated readme in user scripts
charliesimkin Jan 11, 2024
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2 changes: 1 addition & 1 deletion snakemake/wrangler_by_sample_setup.smk
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Expand Up @@ -44,7 +44,7 @@ rule generate_mip_files:
'''
input:
arms_file='/opt/project_resources/mip_ids/mip_arms.txt',
sample_sheet='/opt/input_sample_sheet_directory/'+config['input_sample_sheet_name'],
sample_sheet='/opt/input_sample_sheet_directory/'+config['input_sample_sheet'].split('/')[-1],
fastq_folder='/opt/data'
params:
sample_set=config['sample_set_used'],
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13 changes: 13 additions & 0 deletions user_scripts/wrangler_by_sample.sh
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Expand Up @@ -29,8 +29,20 @@ function parse_yaml {
}'
}


eval $(parse_yaml wrangler_by_sample.yaml)

function parse_sample_sheet_directory {
readarray -d "/" -t strarr <<< "$input_sample_sheet"
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This is a cool Unix function for splitting up a string into an array. I'll have to try and remember this, thanks for sharing it

for (( n=1; n < ${#strarr[*]}-1; n++))
do
input_sample_sheet_directory+="/${strarr[n]}"
done
echo $input_sample_sheet_directory
}
input_sample_sheet_directory=$(parse_sample_sheet_directory)


############################
# setup the run
##########################
Expand All @@ -43,6 +55,7 @@ singularity_bindings="-B $project_resources:/opt/project_resources
-B $output_folder:/opt/analysis
-B $input_sample_sheet_directory:/opt/input_sample_sheet_directory
-B $fastq_dir:/opt/data
-B /home/charlie/projects/MIPTools_wrangler_in_sif/snakemake:/opt/snakemake
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I'm hoping this path isn't hardcoded into the final shell script. Will look for a future commit that removes it

-H $newhome"

snakemake_args="--cores $cpu_count --keep-going --rerun-incomplete --latency-wait 60"
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8 changes: 3 additions & 5 deletions user_scripts/wrangler_by_sample.yaml
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Expand Up @@ -13,7 +13,7 @@ downsample_seed: 312
#how many CPUs (or threads) to use in parallel - you can set this relatively low
#(e.g. 10) because most of the intensive steps of this program are parallelized
#across samples (i.e. 1000 parallel processes if you have 1,000 samples).
cpu_count: 5
cpu_count: 16

#This applies to the most memory intensive steps of the pipeline. Lower values
#complete faster on a cluster but may crash out for bigger samples or highly
Expand All @@ -24,9 +24,7 @@ cpu_count: 5
memory_mb_per_step: 20000

#location of sample sheet
input_sample_sheet_directory: /home/charlie/projects/miptools_data/miptools_test-data/test_data

input_sample_sheet_name: sample_list.tsv
input_sample_sheet: /home/charlie/projects/miptools_data/miptools_test-data/test_data/sample_list.tsv
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This is a nice fix - decreases the number of variables a user has to enter into the yaml file


#location of project resources
project_resources: /home/charlie/projects/miptools_data/miptools_test-data/DR1_project_resources
Expand All @@ -35,7 +33,7 @@ project_resources: /home/charlie/projects/miptools_data/miptools_test-data/DR1_p
fastq_dir: /home/charlie/projects/miptools_data/miptools_test-data/test_data/fastq

#location of sif file to use
miptools_sif: /home/charlie/Downloads/MIPTools/wrangler_in_sif.sif
miptools_sif: /home/charlie/projects/miptools_data/wrangler_in_sif.sif

#only rows from the sample sheet that contain exact matches to the probe sets
#listed here (after splitting the probe_set column with commas) will be analyzed
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