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condition for running process (#153)
* add condition for run process * add resquiggle processors param * add other docker env
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,145 @@ | ||
| /* | ||
| ========================================================================================= | ||
| NANOME(Nanopore methylation) pipeline for Oxford Nanopore sequencing | ||
| ========================================================================================= | ||
| NANOME Analysis Pipeline. | ||
| #### Homepage / Documentation | ||
| https://github.com/LabShengLi/nanome | ||
| @Author : Yang Liu | ||
| @FileName : DEEPSIGNAL2.nf | ||
| @Software : NANOME project | ||
| @Organization : JAX Sheng Li Lab | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
| process DEEPSIGNAL2 { | ||
| tag "${params.dsname}" | ||
|
|
||
| publishDir "${params.outdir}/${params.dsname}-methylation-callings/Raw_Results-${params.dsname}", | ||
| mode: "copy", | ||
| pattern: "${params.dsname}_deepsignal2_per_read_combine.*.gz", | ||
| enabled: params.outputRaw | ||
|
|
||
| publishDir "${params.outdir}/${params.dsname}-methylation-callings/Features-${params.dsname}", | ||
| mode: "copy", | ||
| pattern: "${params.dsname}_deepsignal2_feature_combine.*.gz" | ||
|
|
||
| input: | ||
| path resquiggle_collect | ||
| // path feature_collect | ||
| path reference_genome | ||
| path ch_src | ||
| path ch_utils | ||
|
|
||
| output: | ||
| path "${params.dsname}_deepsignal2_per_read_combine.*.gz", emit: deepsignal2_combine_out | ||
| path "${params.dsname}_deepsignal2_feature_combine.*.gz", emit: deepsignal2_feature_out, optional: true | ||
|
|
||
| when: | ||
| params.runMethcall && params.runDeepSignal2 | ||
|
|
||
| script: | ||
| cores = task.cpus * params.highProcTimes | ||
|
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||
| shell: | ||
| ''' | ||
| set +xu | ||
| . /opt/conda/etc/profile.d/conda.sh | ||
| conda activate /opt/conda/envs/deepsignal2 | ||
| set -x | ||
| export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH | ||
| export HDF5_PLUGIN_PATH="$CONDA_PREFIX/hdf5/lib/plugin" | ||
| which deepsignal2 | ||
| wget !{params.DEEPSIGNAL2_MODEL_FILE} | ||
| tar -xzf !{params.DEEPSIGNAL2_MODEL_NAME}.tar.gz | ||
| echo "CUDA_VISIBLE_DEVICES=${CUDA_VISIBLE_DEVICES:-}" | ||
| if [[ "${CUDA_VISIBLE_DEVICES:-}" == "" ]] ; then | ||
| echo "Detect no GPU, using CPU commandType" | ||
| commandType='cpu' | ||
| gpuOptions=" " | ||
| else | ||
| echo "Detect GPU, using GPU commandType" | ||
| commandType='gpu' | ||
| gpuOptions="--nproc_gpu 1" | ||
| fi | ||
| > !{params.dsname}_deepsignal2_feature_combine.tsv.gz | ||
| > !{params.dsname}_deepsignal2_per_read_combine.tsv.gz | ||
| find . -maxdepth 1 -name '*.resquiggle' -print0 | | ||
| while IFS= read -r -d '' infn; do | ||
| deepsignal2 extract \ | ||
| -i ${infn}/workspace/ \ | ||
| -o ${infn}_feature.tsv \ | ||
| --corrected_group RawGenomeCorrected_000 \ | ||
| --nproc !{cores} --motifs CG \ | ||
| &>> !{params.dsname}.DeepSignal2.run.log | ||
| deepsignal2 call_mods \ | ||
| --model_path !{params.DEEPSIGNAL2_MODEL_NAME} \ | ||
| --input_path ${infn}_feature.tsv \ | ||
| --result_file ${infn/.resquiggle/_deepsignal2_batch_per_read.tsv} \ | ||
| --nproc !{cores} ${gpuOptions} \ | ||
| &>> !{params.dsname}.DeepSignal2.run.log | ||
| cat ${infn}_feature.tsv | gzip -f >> \ | ||
| !{params.dsname}_deepsignal2_feature_combine.tsv.gz | ||
| cat ${infn/.resquiggle/_deepsignal2_batch_per_read.tsv} | gzip -f >> \ | ||
| !{params.dsname}_deepsignal2_per_read_combine.tsv.gz | ||
| done | ||
| echo "### DeepSignal2 methylation DONE" | ||
| if [[ !{params.deduplicate} == true ]] ; then | ||
| echo "### Deduplicate for read-level outputs" | ||
| ## sort order: Chr, Start, (End), ID, Strand | ||
| zcat !{params.dsname}_deepsignal2_per_read_combine.tsv.gz |\ | ||
| sort -V -u -k1,1 -k2,2n -k5,5 -k3,3 |\ | ||
| gzip -f > !{params.dsname}_deepsignal2_per_read_combine.sort.tsv.gz | ||
| rm !{params.dsname}_deepsignal2_per_read_combine.tsv.gz &&\ | ||
| mv !{params.dsname}_deepsignal2_per_read_combine.sort.tsv.gz \ | ||
| !{params.dsname}_deepsignal2_per_read_combine.tsv.gz | ||
| fi | ||
| echo "### DeepSignal2 all combine DONE" | ||
| ''' | ||
| } | ||
|
|
||
| process DEEPSIGNAL2COMB { | ||
| tag "${params.dsname}" | ||
|
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| publishDir "${params.outdir}/${params.dsname}-methylation-callings", | ||
| mode: "copy", | ||
| pattern: "Read_Level-${params.dsname}/${params.dsname}_*-perRead-score*.gz" | ||
|
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| publishDir "${params.outdir}/${params.dsname}-methylation-callings", | ||
| mode: "copy", | ||
| pattern: "Site_Level-${params.dsname}/*-perSite-cov1*.gz" | ||
|
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| input: | ||
| path deepsignal2_combine_out | ||
| path ch_src | ||
| path ch_utils | ||
|
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| output: | ||
| path "Read_Level-${params.dsname}/${params.dsname}_*-perRead-score*.gz", emit: read_unify | ||
| path "Site_Level-${params.dsname}/*-perSite-cov*.gz", emit: site_unify | ||
|
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| when: | ||
| params.runCombine | ||
|
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| script: | ||
| cores = task.cpus * params.highProcTimes | ||
|
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| shell: | ||
| ''' | ||
| ## Unify format output | ||
| bash utils/unify_format_for_calls.sh \ | ||
| !{params.dsname} DeepSignal2 DeepSignal\ | ||
| !{deepsignal2_combine_out} \ | ||
| . !{cores} 12 !{params.sort ? true : false} \ | ||
| "!{params.chrSet1.replaceAll(',', ' ')}" | ||
| ''' | ||
| } |
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