DDA MS proteomics pipeline report

<% out << libs.join('\n') %>

DDA MS proteomics pipeline report

<% out << runname %>

Completed at {{ reportdate }}

Pipeline version {{ version }} DOI{{ doi }}

Results
PSMs
Peptides/proteins/genes
PTMs
Expression
Run data

{% if warnings|length %}

Warnings

• {{ warn }}

{% endif %}

Identification summary

{% for field in summary_fields %} {% endfor %} {% for setname in summary_table %} {% for field in summary_fields %} {% endfor %} {% endfor %}

Experiment set	{{ tabletitles[field] }}
{{ setname }}	{{ summary_table[setname][field] }}

Overlap

{% for fname, ftitle in featnames %} {% if overlap[fname] %}

{% for nr_sets in overlap[fname] %} {% endfor %}

ID in # sets	Amount {{ fname }}
{{ nr_sets }}	{{ overlap[fname][nr_sets] }}

{% endif %} {% endfor %}

{% if ptmtables.summary %}

PTMs

Summary

{% for field in ptmtitles.summary %} {% endfor %} {% for row in ptmtables.summary %} {% for field in ptmtitles.summary %} {% endfor %} {% endfor %}

{{ field }}
{{ row[field] }}

{% if ptmtables.overlap %}

Overlap

{% for field in ptmtitles.overlap %} {% endfor %} {% for row in ptmtables.overlap %} {% for field in ptmtitles.overlap %} {% endfor %} {% endfor %}

{{ field }}
{{ row[field] }}

{% endif %}

Site count

{% for field in ptmtitles.featcount %} {% endfor %} {% for row in ptmtables.featcount %} {% for field in ptmtitles.featcount %} {% endfor %} {% endfor %}

{{ field }}
{{ row[field] }}

{% endif %} {% if normfacs %}

Median centered isobaric normalization factors

{% for fname, ftitle in featnames %} {% if normfacs[fname] %}

{% for setn, ch, nf in normfacs[fname] %} {% endfor %}

Experiment set	Channel	Norm. factor
{{ setn }}	{{ ch }}	{{ nf }}

{% endif %} {% endfor %}

{% endif %}

Software versions

<% out << sw_versions.collect { "" }.join("\n") %>

Software	Version	Container
${it[0]}	${it[1]}	${it[2]}

Non-default parameters

<% out << params.collect { "" }.join("\n") %>

Parameter	Value
`--${it.key}`	`${it.value}`

Input files

<% out << infiles[0].collect { "" }.join('\n') %> <% out << infiles[1..-1].collect { " ${it.collect{x -> "" }.join('\n')}" }.join('\n') %>

${it}
${x}

# of PSMs and scans

# of missed cleavages

{% if plots.isomissvals %}

Isobaric missing values

{% endif %}

{% if plateplots.fryield %}

Fraction yield

{% for p in plates %} {% if plateplots.fryield[p] %}

Plate: {{ p }}

{{ plateplots.fryield[p] }} {% endif %} {% endfor %} {% endif %} {% if plateplots.precerror %}

Precursor error

{% for p in plates %} {% if plateplots.precerror[p] %}

Plate: {{ p }}

{{ plateplots.precerror[p] }} {% endif %} {% endfor %} {% endif %} {% if plateplots.score %}

Search engine score

{% for p in plates %} {% if plateplots.score[p] %}

Plate: {{ p }}

{{ plateplots.score[p] }} {% endif %} {% endfor %} {% endif %} {% if plateplots.retentiontime %}

Retention time

{% for p in plates %} {% if plateplots.retentiontime[p] %}

Plate: {{ p }}

{{ plateplots.retentiontime[p] }} {% endif %} {% endfor %} {% endif %} {% if plateplots.ioninjtime %}

Ion injection time

{% for p in plates %} {% if plateplots.ioninjtime[p] %}

Plate: {{ p }}

{{ plateplots.ioninjtime[p] }} {% endif %} {% endfor %} {% endif %} {% if plateplots.pif %}

Precursor purity

{% for p in plates %} {% if plateplots.pif[p] %}

Plate: {{ p }}

{{ plateplots.pif[p] }} {% endif %} {% endfor %} {% endif %}

{% for plotname, plottitle in featplotnames %} {% if featplots[plotname] %}

{% for fname, ftitle in featnames %} {% if featplots[plotname][fname] %}

{% for line in featplots[plotname][fname + '__text'] %}

{% endfor %} {{ featplots[plotname][fname] }}

{% endif %} {% endfor %}

{% if ptmtables.summary %}

PTM numbers

{% for ftitle, plot in ptmplots.feats.items() %}

{% endfor %}

PTM residue distributions

{% for ftitle, plot in ptmplots.residues.items() %}

{% endfor %}

{% endif %} {% if expplots.pca %}

{% for plotname, plottitle in expplotnames %}

{% for fname, ftitle in featnames %} {% if expplots[plotname][fname] %}

{% endif %} {% endfor %}

{% endfor %} {% if deqmsplots %}

DEqMS results

{% for fname, ftitle in featnames %} {% if deqmsplots[fname] %}

{{ ftitle }}
{% for comp in deqmscomps %} {% if deqmsplots[fname][comp] %}
{% endif %} {% endfor %}
{% endif %} {% endfor %}
{% endif %}

{% endif %}