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fix: mTRAQ #73

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fix: mTRAQ #73

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5 changes: 5 additions & 0 deletions modules/local/diann/assemble_empirical_library/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,9 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
diann_im_window = params.im_window ? "--im-window $params.im_window" : ""
diann_dda_flag = meta.acquisition_method == 'dda' ? "--dda" : ""

diann_channel_run_norm = params.channel_run_norm ? "--channel-run-norm" : ""
diann_channel_spec_norm = params.channel_spec_norm ? "--channel-spec-norm" : ""

"""
# Precursor Tolerance value was: ${meta['precursormasstolerance']}
# Fragment Tolerance value was: ${meta['fragmentmasstolerance']}
Expand Down Expand Up @@ -76,6 +79,8 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
${diann_tims_sum} \\
${diann_im_window} \\
${diann_dda_flag} \\
${diann_channel_run_norm} \\
${diann_channel_spec_norm} \\
\${mod_flags} \\
$args \\
2>&1 | tee assemble_empirical_library.log
Expand Down
5 changes: 5 additions & 0 deletions modules/local/diann/individual_analysis/main.nf
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Expand Up @@ -88,6 +88,9 @@ process INDIVIDUAL_ANALYSIS {
min_fr_mz = meta['ms2minmz'] ? "--min-fr-mz ${meta['ms2minmz']}" : ""
max_fr_mz = meta['ms2maxmz'] ? "--max-fr-mz ${meta['ms2maxmz']}" : ""

diann_channel_run_norm = params.channel_run_norm ? "--channel-run-norm" : ""
diann_channel_spec_norm = params.channel_spec_norm ? "--channel-spec-norm" : ""

"""
# Extract --var-mod, --fixed-mod, and --monitor-mod flags from diann_config.cfg
mod_flags=\$(grep -oP '(--var-mod\\s+\\S+|--fixed-mod\\s+\\S+|--monitor-mod\\s+\\S+|--lib-fixed-mod\\s+\\S+|--original-mods|--channels\\s+.+)' ${diann_config} | tr '\\n' ' ')
Expand All @@ -114,6 +117,8 @@ process INDIVIDUAL_ANALYSIS {
${diann_tims_sum} \\
${diann_im_window} \\
${diann_dda_flag} \\
${diann_channel_run_norm} \\
${diann_channel_spec_norm} \\
\${mod_flags} \\
$args \\
2>&1 | tee ${ms_file.baseName}_final_diann.log
Expand Down
5 changes: 5 additions & 0 deletions modules/local/diann/preliminary_analysis/main.nf
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Expand Up @@ -69,6 +69,9 @@ process PRELIMINARY_ANALYSIS {
min_fr_mz = meta['ms2minmz'] ? "--min-fr-mz ${meta['ms2minmz']}" : ""
max_fr_mz = meta['ms2maxmz'] ? "--max-fr-mz ${meta['ms2maxmz']}" : ""

diann_channel_run_norm = params.channel_run_norm ? "--channel-run-norm" : ""
diann_channel_spec_norm = params.channel_spec_norm ? "--channel-spec-norm" : ""

"""
# Precursor Tolerance value was: ${meta['precursormasstolerance']}
# Fragment Tolerance value was: ${meta['fragmentmasstolerance']}
Expand Down Expand Up @@ -99,6 +102,8 @@ process PRELIMINARY_ANALYSIS {
${diann_im_window} \\
--no-prot-inf \\
${diann_dda_flag} \\
${diann_channel_run_norm} \\
${diann_channel_spec_norm} \\
\${mod_flags} \\
$args \\
2>&1 | tee ${ms_file.baseName}_diann.log
Expand Down
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