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Multiqc 1.35#1722

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erinyoung merged 1 commit into
StaPH-B:masterfrom
RaheelSyedAhmed:multiqc-1.35
Jun 26, 2026
Merged

Multiqc 1.35#1722
erinyoung merged 1 commit into
StaPH-B:masterfrom
RaheelSyedAhmed:multiqc-1.35

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@RaheelSyedAhmed

@RaheelSyedAhmed RaheelSyedAhmed commented Jun 25, 2026

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Pull Request (PR) checklist:

  • Include a description of what is in this pull request in this message.
  • The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15 )
  • Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/spades/3.12.0/README.md)
    • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
  • Dockerfile includes the recommended LABELS
  • Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
  • Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

PR Description:
Updated Dockerfile to use MULTIQC_VER=1.35 and added version command in the test stage. Added python packages installed by pip in the program-specific README.md. Added version 1.35 in the versions dropdown entry for multiqc. No changes in the program license were found.

@RaheelSyedAhmed
Updated Dockerfile to use MULTIQC_VER=1.35 and added version command …
6a7c152 
…in the test stage. Added python packages installed by pip in the program-specific README.md. Added version 1.35 in the versions dropdown entry for multiqc.
@erinyoung

erinyoung commented Jun 26, 2026

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@staphb-dockerbuilds-diff multiqc 1.34 1.35

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github-actions Bot commented Jun 26, 2026

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Dockerfile Diff: multiqc

Comparing: 1.34 -> 1.35

--- build-files/multiqc/1.34/Dockerfile	2026-06-26 18:48:06.283024933 +0000
+++ build-files/multiqc/1.35/Dockerfile	2026-06-26 18:48:06.283121944 +0000
@@ -1,6 +1,6 @@
 FROM ubuntu:noble AS app
 
-ARG MULTIQC_VER="1.34"
+ARG MULTIQC_VER="1.35"
 
 # metadata
 LABEL base.image="ubuntu:noble"
@@ -35,7 +35,7 @@
 RUN apt-get update && apt-get install -y git
 
 # to ensure multiqc is in PATH
-RUN multiqc --help
+RUN multiqc --version && multiqc --help
 
 # set working directory so that all test inputs & outputs are kept in /test
 RUN mkdir /test

@erinyoung

erinyoung commented Jun 26, 2026

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Looks like this works. There's something wrong with bclconvert, but I think that's a multiqc thing and not something we could fix in the image.

#14 [test 5/6] RUN git clone https://github.com/ewels/MultiQC_TestData &&     multiqc . &&     ls multiqc_report.html
#14 0.049 Cloning into 'MultiQC_TestData'...
#14 8.016 Updating files:  85% (2433/2837)
Updating files:  86% (2440/2837)
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Updating files: 100% (2837/2837)
Updating files: 100% (2837/2837), done.
#14 9.626 
#14 9.626 /// MultiQC 🔍 v1.35
#14 9.626 
#14 10.18        file_search | Search path: /test
#14 14.44        bases2fastq | Skipping Bases2Fastq-Sim-b2f__sample_0 because it has <1000 assigned reads [n=39].
#14 14.44        bases2fastq | Skipping Bases2Fastq-Sim-b2f__sample_1 because it has <1000 assigned reads [n=43].
#14 14.44        bases2fastq | Skipping Bases2Fastq-Sim-b2f__sample_2 because it has <1000 assigned reads [n=38].
#14 14.44        bases2fastq | Skipping Bases2Fastq-Sim-b2f__sample_3 because it has <1000 assigned reads [n=37].
#14 14.44        bases2fastq | Skipping Bases2Fastq-Sim-b2f__sample_4 because it has <1000 assigned reads [n=38].
#14 15.13        bases2fastq | Skipping SI464-6f93__UDI_8 because it has <1000 assigned reads [n=0].
#14 15.58        bases2fastq | Skipping Bases2Fastq-Sim-b2f__sample_0 because it has <1000 assigned reads [n=39].
#14 15.58        bases2fastq | Skipping Bases2Fastq-Sim-b2f__sample_1 because it has <1000 assigned reads [n=43].
#14 15.58        bases2fastq | Skipping Bases2Fastq-Sim-b2f__sample_2 because it has <1000 assigned reads [n=38].
#14 15.58        bases2fastq | Skipping Bases2Fastq-Sim-b2f__sample_3 because it has <1000 assigned reads [n=37].
#14 15.58        bases2fastq | Skipping Bases2Fastq-Sim-b2f__sample_4 because it has <1000 assigned reads [n=38].
#14 16.65        bases2fastq | Found 8 run(s) within the Bases2Fastq results.
#14 16.65        bases2fastq | Found 4 project(s) within the Bases2Fastq results.
#14 16.65        bases2fastq | Found 128 sample(s) within the Bases2Fastq results.
#14 19.53     cellranger_arc | Found 2 Cell Ranger ARC reports
#14 19.61        cells2stats | Found 1 samples within the cells2stats results
#14 19.69           hicstuff | Found 5 pipeline reports
#14 19.69           hicstuff | Found 3 distance-law files
#14 19.72       hifi_trimmer | Found 3 reports
#14 19.81         methurator | No sample data found in methurator_summary.yml
#14 19.82         methurator | Found 1 samples
#14 19.84           ribotish | Found 3 Ribo-TISH reports
#14 19.86          ribowaltz | Found 1 samples
#14 19.91              riker | Found 2 riker alignment reports
#14 19.95              riker | Found 2 riker basic reports
#14 19.96              riker | Found 1 riker gcbias reports
#14 19.98              riker | Found 1 riker hybcap reports
#14 20.00              riker | Found 2 riker isize reports
#14 20.03              riker | Found 1 riker wgs reports
#14 20.06             seqkit | Found 6 stats reports
#14 20.06              sompy | Found 1 sompy reports
#14 20.10             xenium | Found 4 Xenium reports
#14 20.10             xenium | Sample 'sample3' has low transcript assignment rate: 0.580 (< 0.7). Cell segmentation likely needs refinement.
#14 20.10             xenium | Run 'pip install multiqc-xenium-extra' for additional visualizations
#14 20.15     custom_content | ivar_variants: Found 1 samples (PlotType.BAR)
#14 20.15     custom_content | Test-Mire2: Found 1 sample (image)
#14 33.00         bclconvert | Sample MDX200159_L2000801 has different indices on different lanes: GTCGGAGC-GGTTATAA != None, overriding
#14 33.00         bclconvert | Sample PTC_Tsqn200928MB_L2000806 has different indices on different lanes: GGCATTCT-CTAGCTTG != None, overriding
#14 33.00         bclconvert | Sample NTC_Tsqn200928MB_L2000807 has different indices on different lanes: AATGCCTC-TCGATCCA != None, overriding
#14 33.00         bclconvert | Sample PRJ200431_L2000811 has different indices on different lanes: CGGCATTA-GTCAGTCA != None, overriding
#14 33.00         bclconvert | Sample PRJ200442_L2000812 has different indices on different lanes: CACGCAAT-CCTTCCAT != None, overriding
#14 33.00         bclconvert | Sample NTC_NebRNA200929_L2000813 has different indices on different lanes: GGAATGTC-AGGAACAC != None, overriding
#14 33.00         bclconvert | Sample PRJ200434_L2000814 has different indices on different lanes: TGGTGAAG-CTTACAGC != None, overriding
#14 33.00         bclconvert | Sample PRJ200437_L2000815 has different indices on different lanes: GGACATCA-TACCTGCA != None, overriding
#14 33.00         bclconvert | Sample PRJ200440_L2000816 has different indices on different lanes: GGTGTACA-AGACGCTA != None, overriding
#14 33.00         bclconvert | Sample PRJ200441_L2000817 has different indices on different lanes: GATAGCCA-CAACACAG != None, overriding
#14 33.00         bclconvert | Sample PRJ200443_L2000818 has different indices on different lanes: CCACAACA-GTACCACA != None, overriding
#14 33.00         bclconvert | Sample PRJ200445_L2000819 has different indices on different lanes: GGCTTACT-CTTTCCCT != None, overriding
#14 33.00         bclconvert | Sample PRJ200464_L2000820 has different indices on different lanes: ACGATATG-GACAATTC != None, overriding
#14 33.00         bclconvert | Sample PRJ200466_L2000821 has different indices on different lanes: ATCCGCAG-ACACGACT != None, overriding
#14 33.00         bclconvert | Sample PRJ200468_L2000822 has different indices on different lanes: TTCAATAG-TCCCACGA != None, overriding
#14 33.00         bclconvert | Sample PRJ200476_L2000823 has different indices on different lanes: GTTTGCTC-ACCAACAG != None, overriding
#14 33.00         bclconvert | Sample PTC_NebRNA200929_L2000824 has different indices on different lanes: AGAAGCCT-GTCAGTAT != None, overriding
#14 33.00         bclconvert | Sample PTC_TSOctDNA200901VD_L2000753 has different indices on different lanes: CCGTGACCGA-CCGAACGTTG != None, overriding
#14 33.00         bclconvert | Sample PTC_TSOctDNA200901VD_L2000754 has different indices on different lanes: ATACTTGTTC-TAACCGCCGA != None, overriding
#14 33.00         bclconvert | Sample PTC_TSOctDNA200901VD_L2000755 has different indices on different lanes: TCCGCCAATT-CTCCGTGCTG != None, overriding
#14 33.00         bclconvert | Sample NTC_TSOctDNA200901VD_L2000756 has different indices on different lanes: AGGACAGGCC-CATTCCAGCT != None, overriding
#14 33.00         bclconvert | Sample PRJ200438_LPRJ200438 has different indices on different lanes: CATGCGAT != None, overriding
#14 33.00         bclconvert | Sample PRJ200438_LPRJ200438 has different indices on different lanes: TGATATTC != CATGCGAT, overriding
#14 33.00         bclconvert | Sample PRJ200438_LPRJ200438 has different indices on different lanes: GTGATCGA != TGATATTC, overriding
#14 33.00         bclconvert | Sample PRJ200438_LPRJ200438 has different indices on different lanes: ACCCGACG != GTGATCGA, overriding
#14 33.00         bclconvert | Sample PRJ200439_LPRJ200439 has different indices on different lanes: GCAACAAA != None, overriding
#14 33.00         bclconvert | Sample PRJ200439_LPRJ200439 has different indices on different lanes: TAGTTGTC != GCAACAAA, overriding
#14 33.00         bclconvert | Sample PRJ200439_LPRJ200439 has different indices on different lanes: CGCCATCG != TAGTTGTC, overriding
#14 33.00         bclconvert | Sample PRJ200439_LPRJ200439 has different indices on different lanes: ATTGGCGT != CGCCATCG, overriding
#14 33.00         bclconvert | Sample quantseq_pool_202404 has different project names on different lanes: HGL_Cancer_Met_Mechanisms != None, overriding
#14 33.00         bclconvert | Sample quantseq_pool_202404 has different indices on different lanes:  != None, overriding
#14 33.00         bclconvert | Sample S34863_GBC_Multiplex has different indices on different lanes: ACAGGGCTAC-GAGCATCTAT != None, overriding
#14 33.00         bclconvert | Found runs: 237, samples: 237
#14 33.01         bclconvert | Found multiple sequencer runs, do not report undetermined stats
#14 33.36            interop | Found 3 reports
#14 33.44               ivar | Found 3 reports
#14 33.56              flash | Found 5 log reports
#14 33.57              flash | Found 4 histogram reports
#14 33.58          seqyclean | Found 6 logs
#14 33.61           optitype | Found 1 reports
#14 33.62           whatshap | Could not find the 'ALL' chromosome for GM24385_0_1x_full_opt_trunc. Make sure that the input is not truncated. MultiQC will summarize information for all available chromosomes instead.
#14 33.89        spaceranger | Found 7 Space Ranger count reports
#14 33.90             xenome | Found 3 reports
#14 33.93           xengsort | Found 1 reports
#14 33.95          metaphlan | Found 1 reports
#14 33.97           sylphtax | Found 2 reports
#14 33.98             seqwho | Found 1 reports
#14 34.01             telseq | Found 9 reports
#14 34.12              ataqv | Found 6 reports
#14 34.21              ataqv | Error adding FLD distance plot: 'fragment_length_distance'
#14 34.23             mgikit | 1 general information log files (*.mgikit.sample_stats) were loaded
#14 34.24             mgikit | 1 read information log files (*.mgikit.info) were loaded
#14 34.27             mgikit | 1 undetermined barcode log files (*.mgikit.undetermined_barcode) were loaded
#14 34.28             mgikit | 1 ambiguous barcode log files (*.mgikit.ambiguous_barcode) were loaded
#14 34.29       mosaicatcher | Found 96 reports
#14 34.50      write_results | Rendering plots. Some plots rendered flat because the number of series exceeds 2000, and this rendering might take a while. To disable, set `--interactive` (`plots_force_interactive: true` in config), or change the `plots_flat_numseries` to a higher value
#14 56.50      write_results | Data        : multiqc_data
#14 59.57      write_results | Report      : multiqc_report.html
#14 59.57            multiqc | MultiQC complete

erinyoung
erinyoung approved these changes Jun 26, 2026
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@erinyoung erinyoung left a comment

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I have no changes to recommend. Let's get this merged and deployed!

@erinyoung erinyoung merged commit f70de5f into StaPH-B:master Jun 26, 2026
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@erinyoung

erinyoung commented Jun 26, 2026

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The status of the deploy can be found here : https://github.com/StaPH-B/docker-builds/actions/runs/28259612917

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@RaheelSyedAhmed @erinyoung