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Amplicon Illumina nextflow conversion: Added Python wrapper script #133

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1702918
Fixed group means and stds
olabiyi Nov 18, 2024
8a7bbaa
set ANCOMBC image to 2.6.0
olabiyi Nov 18, 2024
a4d1505
added run workflow script
olabiyi Nov 27, 2024
7a97404
Edited README
olabiyi Nov 27, 2024
f7df02f
Edited README
olabiyi Nov 27, 2024
addf4d6
Fixed no extra argument to nextflow bug
olabiyi Nov 28, 2024
7a9c637
updated UNITE_DB link
olabiyi Dec 5, 2024
10afc84
added deseq
olabiyi Dec 24, 2024
b8ea788
Fixed beta diversity
olabiyi Dec 24, 2024
51bdac9
Updated pipeline document
olabiyi Jan 2, 2025
0f68848
Added more comments to pipeline document
olabiyi Jan 3, 2025
d1670ff
Fixed taxize's api rate error
olabiyi Jan 6, 2025
e579cba
fixed post processing bug
olabiyi Jan 6, 2025
e48589a
Added remove rare functionality
olabiyi Jan 8, 2025
b61a9b5
updated nextflow version
olabiyi Jan 8, 2025
1998ed2
Fixed reads count column bug
olabiyi Jan 8, 2025
e11e03f
Updated readme and variables
olabiyi Jan 9, 2025
4c44697
Fixed software versions redundancy bug
olabiyi Jan 10, 2025
39bd0f2
Added diversity and differential abundance testing to README post-pro…
olabiyi Jan 13, 2025
409b6f8
updated pipeline document
olabiyi Jan 15, 2025
5b74691
updated pipeline document
olabiyi Jan 15, 2025
3657ba5
Documented functions
olabiyi Jan 18, 2025
7cc24dc
assigned a default value to params.help
olabiyi Jan 21, 2025
6923766
Added some more comments to preprocessing
olabiyi Jan 23, 2025
9a7726a
Formatting changes
bnovak32 Feb 21, 2025
8e94dc9
Added structural zeros removal functionality
olabiyi Feb 22, 2025
d53e371
Renamed volcano plots
olabiyi Feb 24, 2025
e5b6882
Merge pull request #1 from bnovak32/DEV_Amplicon_Illumina_NF_conversi…
olabiyi Feb 25, 2025
b707346
Updated the pipeline document
olabiyi Feb 27, 2025
483b939
Updated the pipeline document
olabiyi Feb 27, 2025
d48eb0f
Updated the pipeline document
olabiyi Feb 27, 2025
b202b79
Updated volcano plots file name
olabiyi Feb 28, 2025
e92025e
fixed minor bugs
olabiyi Feb 28, 2025
6c6bfef
Edited launchDir for post-processing
olabiyi Feb 28, 2025
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assigned a default value to params.help
olabiyi committed Jan 21, 2025
commit 7cc24dc97237a7d44cc06edada1ba39c0f2edb60
Original file line number Diff line number Diff line change
@@ -7,6 +7,8 @@ c_bright_green = "\u001b[32;1m";
c_blue = "\033[0;34m";
c_reset = "\033[0m";

params.help = false

/**************************************************
* HELP MENU **************************************
**************************************************/
Original file line number Diff line number Diff line change
@@ -113,7 +113,6 @@ profiles {
docker {
docker.enabled = true
docker.runOptions = '-u $(id -u):$(id -g)'
docker.userEmulation = true
params.containerEngine = "docker"
}