Skip to content

Commit

Permalink
refactor: Improve styling on MultiQC report (#32)
Browse files Browse the repository at this point in the history 
* fix: Make MultiQC detect diamond logs

* refactor: Remove sample enumerator

* refactor: Update multiqc config with more info

* chore: Update multiqc module
  • Loading branch information
@jvfe
jvfe authored Mar 30, 2024
1 parent fc6877c commit 6ab04ad
Show file tree
Hide file tree
Showing 14 changed files with 243 additions and 36 deletions.
10 changes: 9 additions & 1 deletion assets/multiqc_config.yml
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/dalmolingroup/euryale" target="_blank">dalmolingroup/euryale</a>
analysis pipeline.
analysis pipeline. For information about how to interpret these results, see the
<a href="https://dalmolingroup.github.io/euryale/" target="_blank">documentation</a>.
report_section_order:
"dalmolingroup-euryale-methods-description":
order: -1000
Expand All @@ -9,4 +10,11 @@ report_section_order:
"dalmolingroup-euryale-summary":
order: -1002

custom_logo_url: https://github.com/dalmolingroup/euryale
custom_logo_title: "dalmolingroup/euryale"

sp:
diamond:
fn_re: ".*.diamond.log$"

export_plots: true
4 changes: 1 addition & 3 deletions bin/check_samplesheet.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -123,11 +123,9 @@ def validate_unique_samples(self):
"""
if len(self._seen) != len(self.modified):
raise AssertionError("The pair of sample name and FASTQ must be unique.")
seen = Counter()
for row in self.modified:
sample = row[self._sample_col]
seen[sample] += 1
row[self._sample_col] = f"{sample}_T{seen[sample]}"
row[self._sample_col] = f"{sample}"


def read_head(handle, num_lines=10):
Expand Down
81 changes: 60 additions & 21 deletions modules.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,114 +8,153 @@
"bowtie2/align": {
"branch": "master",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/bowtie2/align/bowtie2-align.diff"
},
"bowtie2/build": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/bowtie2/build/bowtie2-build.diff"
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"diamond/blastx": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/diamond/blastx/diamond-blastx.diff"
},
"diamond/makedb": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/diamond/makedb/diamond-makedb.diff"
},
"fastp": {
"branch": "master",
"git_sha": "37a98dd100d74d9188a272197663587de1331a0e",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/fastp/fastp.diff"
},
"fastqc": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gunzip": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/gunzip/gunzip.diff"
},
"kaiju/kaiju": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/kaiju/kaiju/kaiju-kaiju.diff"
},
"kaiju/kaiju2krona": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"kaiju/kaiju2table": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/kaiju/kaiju2table/kaiju-kaiju2table.diff"
},
"kraken2/kraken2": {
"branch": "master",
"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/kraken2/kraken2/kraken2-kraken2.diff"
},
"krakentools/kreport2krona": {
"branch": "master",
"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/krakentools/kreport2krona/krakentools-kreport2krona.diff"
},
"krona/ktimporttext": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"megahit": {
"branch": "master",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/megahit/megahit.diff"
},
"multiqc": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
"installed_by": [
"modules"
],
"patch": "modules/nf-core/multiqc/multiqc.diff"
},
"samtools/bam2fq": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/samtools/bam2fq/samtools-bam2fq.diff"
},
"samtools/sort": {
"branch": "master",
"git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/samtools/sort/samtools-sort.diff"
},
"untar": {
"branch": "master",
"git_sha": "cc1f997fab6d8fde5dc0e6e2a310814df5b53ce7",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/untar/untar.diff"
}
}
}
}
}
}
}
9 changes: 9 additions & 0 deletions modules/nf-core/diamond/blastx/diamond-blastx.diff
View file

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion modules/nf-core/diamond/blastx/main.nf
View file

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

7 changes: 7 additions & 0 deletions modules/nf-core/multiqc/environment.yml
View file

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

10 changes: 6 additions & 4 deletions modules/nf-core/multiqc/main.nf
View file

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

11 changes: 7 additions & 4 deletions modules/nf-core/multiqc/meta.yml
View file

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

14 changes: 14 additions & 0 deletions modules/nf-core/multiqc/multiqc.diff
View file

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading

0 comments on commit 6ab04ad

Please sign in to comment.