Update FastQC/Falco wrappers to make output of pairs compatible with multiQC by lldelisle · Pull Request #7839 · galaxyproject/tools-iuc

lldelisle · 2026-03-27T15:06:30Z

I handle differently pairs to enable to keep both identifiers in report and therefore be compatible with multiQC directly.

Before, when given a collection: list:paired, it will create one job per fastq and in the report the filename would be forward/reverse for all pairs.
Now, it will create one job per pair and in the report the filename is blabla_forward blabla_reverse blublu_forward blublu_reverse.

FOR CONTRIBUTOR:

I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
License permits unrestricted use (educational + commercial)
This PR adds a new tool or tool collection
This PR updates an existing tool or tool collection
This PR does something else (explain below)

There are two labels that allow to ignore specific (false positive) tool linter errors:

skip-version-check: Use it if only a subset of the tools has been updated in a suite.
skip-url-check: Use it if github CI sees 403 errors, but the URLs work.

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

mvdbeek · 2026-03-27T15:17:28Z

I think we want to encourage use of falco, that is supposed to be a faster drop-in replacement for fastqc, do we also need to update that wrapper ?

lldelisle · 2026-03-27T15:18:02Z

I am doing the same modification on falco wrapper just now.

Make output labels unique to pass lint Co-authored-by: Lucille Delisle <lucille.delisle@unige.ch>

lldelisle · 2026-03-31T10:17:56Z

Here is the new version with a single execution with one or 2 input files as @bgruening suggested.

lldelisle · 2026-04-10T08:36:04Z

@bgruening / @mvdbeek would you have time to have a look?

bgruening

Looks good from my side. Just two small questions.

@wm75 you might want to look at it.

wm75 · 2026-04-10T10:25:49Z

@lldelisle the changes look fine to me, but I'm a bit confused how much this really helps.

Are you thinking of this in conjunction with #2028 ?

Cause without this, the status quo is:

Flatten a list:paired fastq input
Pass the result to fastqc/falco
Run MultiQC on the output

In contrast with the change here, you'd have to do:

Pass a list:paired fastq collection to fastqc
Flatten the resulting list:paired report
Pass that to MultiQC

So you really only save a step if MultiQC can deal with paired collections? Is that what it is, or am I simply wrong?

lldelisle · 2026-04-10T10:37:04Z

You don't need to flatten before giving to MultiQC. You can give to MultiQC the list:paired and the sample name is taken from the report itself not from the identifiers.

lldelisle · 2026-04-10T10:37:33Z

So before:

Flatten
Falco
MultiQC

After:

Falco
MultiQC

lldelisle · 2026-04-10T10:38:52Z

With this PR, we don't need #2028 and we simplify tutorials and workflows

lldelisle · 2026-04-10T10:40:27Z

Currently if you do:

falco
multiQC

The identifier is forward for all forwards and reverse for all reverse, then you get only one result.

Even if you do:

falco
flatten
MultiQC

You get the same result: only one forward and one reverse is displayed.

wm75 · 2026-04-10T11:11:47Z

So before:

* Flatten

* Falco

* MultiQC

After:

* Falco

* MultiQC

I see. I didn't know you could pass a paired collection to MultiQC.
Turns out you can, but only if you're cheating, i.e. by dragging the paired collection over the fastqc raw data input field in the multiqc tool interface. It's not offered by default.
Also the WF editor doesn't allow you to cheat:

So unless MultiQC gets an extension to consume paired data as fastqc raw data explicitly, you will still need the flatten collection step in between to do things properly.

lldelisle · 2026-04-10T11:41:44Z

Mmmh this is unfortunate. I will think about it.

Co-authored-by: Wolfgang Maier <maw.public+github@posteo.de>

lldelisle

Maybe I should change the type of output collection

lldelisle · 2026-04-10T15:53:28Z

-            <filter>generate_summary</filter>
+            <filter>input_type_select['input_type'] == 'individually' and generate_summary</filter>
        </data>
+        <collection name="html_files" format="html" type="paired" label="${tool.name} on ${on_string}: Webpages">


Maybe should be type="list"

lldelisle · 2026-04-10T15:53:37Z

+            <data name="reverse" from_work_dir="*reverse_fastqc_report.html" />
+            <filter>input_type_select['input_type'] == 'paired'</filter>
+        </collection>
+        <collection name="text_files" format="txt" type="paired" label="${tool.name} on ${on_string}: RawData text files">


Maybe should be type="list"

lldelisle · 2026-04-10T15:53:43Z

+            <data name="reverse" from_work_dir="*reverse_fastqc_data.txt" />
+            <filter>input_type_select['input_type'] == 'paired'</filter>
+        </collection>
+        <collection name="summary_files" format="txt" type="paired" label="${tool.name} on ${on_string}: SummaryData text files">


Maybe should be type="list"

lldelisle · 2026-04-10T15:54:40Z

+        <data format="txt" name="text_file"  from_work_dir="output.txt" label="${tool.name} on ${on_string}: RawData" >
+            <filter>input_type_select['input_type'] == 'individually'</filter>
+        </data>
+        <collection name="html_files" format="html" type="paired" label="${tool.name} on ${on_string}: Webpages">


Maybe should be type="list"

lldelisle · 2026-04-10T15:54:48Z

+            <data name="reverse" from_work_dir="output_reverse.html" />
+            <filter>input_type_select['input_type'] == 'paired'</filter>
+        </collection>
+        <collection name="text_files" format="txt" type="paired" label="${tool.name} on ${on_string}: RawData text files">


Maybe should be type="list"

handle differently pairs to enable to keep both identifiers in report

5ad780e

lldelisle mentioned this pull request Mar 27, 2026

Workaround for using paired fastqc out in multiqc #2028

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mvdbeek reviewed Mar 27, 2026

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Comment thread tools/fastqc/rgFastQC.xml Outdated

Apply suggestion from @mvdbeek

e396f5e

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

lldelisle added 2 commits March 27, 2026 17:33

fix URL

70686c2

apply same changes to falco

7f51cdb

lldelisle changed the title ~~Update FastQC wrapper to make output of pairs compatible with multiQC~~ Update FastQC/Falco wrappers to make output of pairs compatible with multiQC Mar 27, 2026

bgruening reviewed Mar 27, 2026

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Comment thread tools/fastqc/rgFastQC.xml Outdated

run falco/fastqc on both inputs at the same time

6bb1899

lldelisle commented Mar 31, 2026

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Comment thread tools/fastqc/rgFastQC.xml Outdated

Comment thread tools/fastqc/rgFastQC.xml Outdated

Apply suggestions from code review

24a5a49

Make output labels unique to pass lint Co-authored-by: Lucille Delisle <lucille.delisle@unige.ch>

bgruening reviewed Apr 10, 2026

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Comment thread tools/falco/falco.xml Outdated

bgruening reviewed Apr 10, 2026

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bgruening reviewed Apr 10, 2026

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lldelisle added 2 commits April 10, 2026 11:07

do not mention slower

c8b48b8

do not allow bam/sam in paired mode

850c0c1

wm75 reviewed Apr 10, 2026

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Comment thread tools/falco/falco.xml Outdated

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Comment thread tools/fastqc/rgFastQC.xml

Comment thread tools/fastqc/rgFastQC.xml

lldelisle and others added 2 commits April 10, 2026 14:41

Improve selector label

9a0fcbe

Co-authored-by: Wolfgang Maier <maw.public+github@posteo.de>

improve selector label in fastqc

c38a1e4

lldelisle added 4 commits April 10, 2026 14:46

use regex in from_work_dir rather than mv steps from @wm75 suggestion

9d27e2d

use regex also for summary

03b426f

do symetric tests between fastqc and falco

8af05ac

add png to zip of html

bd2688c

wm75 reviewed Apr 10, 2026

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Comment thread tools/fastqc/rgFastQC.xml Outdated

fix the Images copy

b9e2c9a

lldelisle commented Apr 10, 2026

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fix linting

5024d02

lldelisle mentioned this pull request Apr 10, 2026

Update FastQC/Falco wrappers to generate 2 outputs in case of pair inputs #7874

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