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replacing projectDir with moduleDir #2 #3

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replacing projectDir with moduleDir #2 #3

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22 changes: 11 additions & 11 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ process gather_matrices {

script:
"""
python ${projectDir}/bin/gather_matrices.py --cr_gene ${cr_gene} --cr_velo ${cr_velo} --cb_h5 ${cb_h5} --gather_mode ${params.gather_mode}
python ${moduleDir}/bin/gather_matrices.py --cr_gene ${cr_gene} --cr_velo ${cr_velo} --cb_h5 ${cb_h5} --gather_mode ${params.gather_mode}
"""
}

Expand All @@ -39,7 +39,7 @@ process run_qc {

script:
"""
python ${projectDir}/bin/qc.py --sample_id ${samp} --metrics_csv ${params.metrics_csv} --celltypist ${params.celltypist_model} --qc_mode ${params.qc_mode} --gath_obj ${gath_out} --gmm_cutoff ${params.gmm_cutoff}
python ${moduleDir}/bin/qc.py --sample_id ${samp} --metrics_csv ${params.metrics_csv} --celltypist ${params.celltypist_model} --qc_mode ${params.qc_mode} --gath_obj ${gath_out} --gmm_cutoff ${params.gmm_cutoff}
"""
}

Expand All @@ -57,7 +57,7 @@ process subset_object {

script:
"""
python ${projectDir}/bin/subset.py --sample_id ${samp} --cr_prefix ${params.cr_prefix} --limits_csv ${params.limits_csv}
python ${moduleDir}/bin/subset.py --sample_id ${samp} --cr_prefix ${params.cr_prefix} --limits_csv ${params.limits_csv}
"""
}

Expand Down Expand Up @@ -85,7 +85,7 @@ process find_doublets {
}

"""
python ${projectDir}/bin/flag_doublet.py --filter ${filter_column} --samp ${samp} --input ${qc_out}
python ${moduleDir}/bin/flag_doublet.py --filter ${filter_column} --samp ${samp} --input ${qc_out}
"""

}
Expand Down Expand Up @@ -116,7 +116,7 @@ process pool_all {

script:
"""
python ${projectDir}/bin/pool_all.py --samples ${samp.join(",")} --objects ${qc_out.join(",")} --ranges ${ranges_out.join(",")}
python ${moduleDir}/bin/pool_all.py --samples ${samp.join(",")} --objects ${qc_out.join(",")} --ranges ${ranges_out.join(",")}
"""
}

Expand Down Expand Up @@ -147,8 +147,8 @@ process finalize_qc {

script:
"""
export BASE_DIR=${projectDir}
python ${projectDir}/bin/finalize_qc.py --obj ${pool_out} --scr ${scr_out.join(",")} --meta ${params.metadata} --qc_mode ${params.qc_mode}
export BASE_DIR=${moduleDir}
python ${moduleDir}/bin/finalize_qc.py --obj ${pool_out} --scr ${scr_out.join(",")} --meta ${params.metadata} --qc_mode ${params.qc_mode}
"""
}

Expand All @@ -174,8 +174,8 @@ process finalize_qc_basic {

script:
"""
export BASE_DIR=${projectDir}
python ${projectDir}/bin/finalize_qc_basic.py --obj ${pool_out} --scr ${scr_out.join(",")} --meta ${params.metadata}
export BASE_DIR=${moduleDir}
python ${moduleDir}/bin/finalize_qc_basic.py --obj ${pool_out} --scr ${scr_out.join(",")} --meta ${params.metadata}
"""
}

Expand All @@ -201,7 +201,7 @@ process integrate {

script:
"""
python ${projectDir}/bin/integration.py --obj ${qc2_out} --batch ${params.batch_key} --n_top_genes ${params.n_top_genes} --from_scautoqc ${params.from_scautoqc}
python ${moduleDir}/bin/integration.py --obj ${qc2_out} --batch ${params.batch_key} --n_top_genes ${params.n_top_genes} --from_scautoqc ${params.from_scautoqc}
"""
}

Expand Down Expand Up @@ -340,7 +340,7 @@ workflow subset {
}

workflow subset_new {
params.rng = "$projectDir/bin/subset.py"
params.rng = "$moduleDir/bin/subset.py"
opt_file = file(params.rng)

Channel.fromPath("${params.SAMPLEFILE}")
Expand Down