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Documentation update and added a full test #67

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Jan 9, 2025
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be1ea6b
added more to README; pushing to GitHub to see how it looks there
RobJY Sep 23, 2024
d3f85c7
fixed README bugs
RobJY Sep 23, 2024
a6d5343
more fixes to README
RobJY Sep 23, 2024
d74397e
another README fix
RobJY Sep 24, 2024
1c1a927
updated usage doc
RobJY Sep 24, 2024
c4cf4ed
just a checkpoint
RobJY Sep 25, 2024
bc1af39
Merge branch 'dev' into documentation
RobJY Sep 25, 2024
47f176d
just saving current state of output.md
RobJY Sep 25, 2024
d552812
added more to usage doc
RobJY Oct 2, 2024
8960f1d
small change to usage doc
RobJY Oct 2, 2024
c82929e
updated and cleaned-up output doc
RobJY Oct 4, 2024
3f205bd
output doc fixes
RobJY Oct 4, 2024
c82de83
lint fixes
RobJY Oct 11, 2024
ae3eb7b
fixed subworkflow publication lint warnings
RobJY Oct 15, 2024
84b0f36
had already fixed last pub related lint message
RobJY Oct 16, 2024
15add0e
added full_test
RobJY Oct 16, 2024
d262c32
updated ci for testing
RobJY Oct 18, 2024
d3b9b4b
ci testing
RobJY Oct 18, 2024
142bfa1
ci testing
RobJY Oct 18, 2024
3903510
ci testing
RobJY Oct 18, 2024
fec00ed
ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
18c1d9b
ci tests
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 18, 2024
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ci testing
RobJY Oct 21, 2024
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ci testing
RobJY Oct 21, 2024
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ci testing
RobJY Oct 21, 2024
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ci testing
RobJY Oct 22, 2024
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ci testing
RobJY Oct 22, 2024
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ci testing
RobJY Oct 22, 2024
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ci testing
RobJY Oct 22, 2024
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ci testing
RobJY Oct 22, 2024
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ci testing
RobJY Oct 22, 2024
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ci testing
RobJY Oct 22, 2024
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ci testing
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ci testing
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ci testing
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ci testing
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ci testing
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ci testing
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ci testing
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ci testing
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ci testing
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ci testing
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ci testing
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ci testing
RobJY Oct 23, 2024
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ci testing
RobJY Oct 24, 2024
8e931c6
ci testing - basicpy & ashlar update
RobJY Oct 28, 2024
0edbee8
Revert "added full_test"
RobJY Oct 31, 2024
09d955b
small change to README.md
RobJY Oct 31, 2024
31a28e7
citation update
RobJY Oct 31, 2024
5c65c21
fixed prettier errors
RobJY Nov 7, 2024
e0a3183
prettier fix
RobJY Nov 7, 2024
aec6769
bug fix: typo in ci.yml
RobJY Nov 7, 2024
425ca72
merged in updated dev
RobJY Dec 3, 2024
8dff15e
lint fix
RobJY Dec 3, 2024
1b29e81
lint fix: updated nextflow version
RobJY Dec 3, 2024
6f3ccb3
lint fix: added run ci on dev push
RobJY Dec 3, 2024
e1d66ae
bug fix: removed extra input to pipline initialization
RobJY Dec 3, 2024
111e48e
Update README.md
RobJY Dec 3, 2024
2a7ee6b
removed documentation from ci push and added some README suggestions
RobJY Dec 3, 2024
dbabae8
Update docs/output.md
RobJY Dec 3, 2024
06cffc9
Update docs/output.md
RobJY Dec 3, 2024
f28e414
Update docs/output.md
RobJY Dec 3, 2024
1cf6d02
Update docs/output.md
RobJY Dec 3, 2024
8431d1d
Update docs/usage.md
RobJY Dec 3, 2024
1f35b8a
Update docs/usage.md
RobJY Dec 3, 2024
37be4cf
Update docs/usage.md
RobJY Dec 3, 2024
0b231b4
a bunch of simple fixes from PR suggestions
RobJY Dec 3, 2024
ea89f60
fixed marker sheet in docs
RobJY Dec 3, 2024
adbec63
added sample sheet cycle_number validation
RobJY Dec 4, 2024
712eb9b
updated citations for pipeline tools
RobJY Dec 10, 2024
5506382
fixed formatting and added MultiQC back to CITATIONS.md
RobJY Dec 10, 2024
e7d62b5
added test data citations
RobJY Dec 17, 2024
03ad364
Update CITATIONS.md
RobJY Jan 6, 2025
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11 changes: 11 additions & 0 deletions CITATIONS.md
Original file line number Diff line number Diff line change
Expand Up @@ -67,3 +67,14 @@
- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

## Test Data

- cycif-tonsil-cycle\*.ome.tif<br>
Human tonsil section 5 μm thick, imaged in four-channel immunofluorescence over three rounds of bleaching and re-staining with different antibodies. Published in https://doi.org/10.1038/s41592-021-01308-y (slide WD-75684-02). These image files each contain a 3 x 3 grid of overlapping four-channel image tiles with dimensions 220 x 180 pixels. The tiles were cropped from a single raw tile taken from one of the original data files. A Python script (https://github.com/labsyspharm/nf-core-test-datasets-build/blob/main/tonsil-cycif/tonsil-cycif.py) was written to extract the synthetic tile fields from an "interesting" region of the single raw tile, generate stage position metadata with random perturbations to approximate the behavior of a real-world microscope stage, and save the images and metadata as an OME-TIFF file.

- cycif-tonsil-dfp.ome.tif, cycif-tonsil-ffp.ome.tif<br>
Dark-field (dfp) and flat-field (ffp) illumination correction profiles for cycif-tonsil-cycle\*.ome.tif. The dfp profile is all zeros and the ffp profile is all ones and thus will not modify the image when applied, but the images are the correct shape for this data.

- cycif-tonsil-channels.csv<br>
A three-column table containing channel number, imaging cycle number, and marker (target of the fluorescently labeled antibody or other stain) for each channel in each imaging cycle, useful for downstream tools expecting channel annotation.
3 changes: 0 additions & 3 deletions subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -287,9 +287,6 @@ def expandSampleRow( row ) {
def toolCitationText() {
// Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
// Uncomment function in methodsDescriptionText to render in MultiQC report
// TODO: not sure of the correct syntax for the ternary operators below.
// Is this ok or does it need to be enclosed in curly braces to make them closures?
// I don't see examples in sarek, rnaseq or other pipelines
def citation_text = [
"Tools used in the workflow included:",
params["illumination"] ? "Basicpy (Peng et al. 2017)," : "",
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