adds SeqFu

[taylorpaisie]

Pull Request (PR) checklist:

• [ X] Include a description of what is in this pull request in this message.
• [ X] 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/samtools/1.15 )
• [ ]X Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • [ ] (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• [ X] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. 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
• [ X] Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• [ X] Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[erinyoung]

My apologies for my delayed response.

I think this looks great!

I did make some changes, though:

• I moved your labels to the 'app' stage (labels don't transfer between stages and they get lost)
• I added a CMD line to your 'app' stage (the CMD line is the default command that is run in a container, and we generally set that as the help message)
• I removed some tools from the apt-get layer of the 'app' stage.
• I added nim's version to the builder stage for "easy" updating later
• I added in the dev's mini.sh tests - which all seem to work except test-check.sh, so I've dropped it (To me, this looks like a dev thing and not an installation issue)

  Testing module: check 
------------------------------------------------------------ 
OK: Checked single end exit status (expected 0, got 0)
OK: Checked single end OK (expected 1, got 1)
OK: Checked single end libtype (expected SE, got SE)
OK: Checked single end sequence count (expected 7, got 7)
OK: Checked BAD single end exit status with --deep (expected 1, got 1)
OK: Counts checking BAD single end exit status with --deep (expected 0, got 1)
OK: Checked BAD paired end exit status with --deep (expected 2, got 2)
OK: Counts checking BAD paired end exit status with --deep (expected 0, got 0)
OK: Checked BAD single end exit status without --deep (expected 1, got 1)
OK: Counts checking BAD single end exit status without --deep (expected 0, got 1)
OK: Checked paired end (expected 1, got 1)
OK: Checked paired end exit status (expected 0, got 0)
OK: Checked paired end libtype (expected PE, got PE)
OK: Checked single end sequence count (2xSE) (expected 14, got 14)
OK: Checked INVALID paired end (expected 0, got 0)
OK: Checked INVALID paired end exit status (got 1)
OK: Checked INVALID paired end libtype (expected PE, got PE)
OK: Checked INVALID paired end sequence count (2xSE) (expected -, got -)
OK: Checked INVALID directory (/test/test/../data//primers) exit status (expected > 0, got 2)
FAIL: Checked INVALID directory line count (got 14 expected 13)
OK      SE      /test/data/primers/16S_flash.extendedFrags.fastq        4306    1989406 0
OK      SE      /test/data/primers/16S_flash.extendedFrags.fastq.gz     4306    1989406 0
OK      SE      /test/data/primers/16S_merge.fq.gz      6137    2596981 0
OK      SE      /test/data/primers/16S_vsearch_merge.fq.gz      3935    1818111 0
ERR     SE      /test/data/primers/artificial.fq.gz     -       -       2       Invalid character in sequence: < > in R2.REV+.middle;
OK      SE      /test/data/primers/its-merge.fq.gz      7299    1504898 0
OK      SE      /test/data/primers/se.fq.gz     234     70434   0
OK      SE      /test/data/primers/small.fq     4       360     0
OK      PE      /test/data/primers/16S_R1.fq.gz 12274   3694474 0
OK      PE      /test/data/primers/16Snano_R1.fq.gz     468     140868  0
ERR     PE      /test/data/primers/art_R1.fq.gz 7       -       4       R2=Invalid character in sequence: < > in R2.REV+.middle;First sequence names do not match (R1.startFOR+, R2.startREV+);Last sequence names do not match (R1.FOR1+.start-middle, );
OK      PE      /test/data/primers/its_R1.fq.gz 16000   3387804 0
OK      PE      /test/data/primers/itsfilt_R1.fq.gz     15618   3272396 0
OK      PE      /test/data/primers/pico_R1.fq.gz        24      7224    0
total 10M
-rw-rw-r-- 1 root root 869K Dec 19  2023 16S_R1.fq.gz
-rw-rw-r-- 1 root root 986K Dec 19  2023 16S_R2.fq.gz
-rw-rw-r-- 1 root root 4.1M Dec 19  2023 16S_flash.extendedFrags.fastq
-rw-rw-r-- 1 root root 606K Dec 19  2023 16S_flash.extendedFrags.fastq.gz
-rw-rw-r-- 1 root root  256 Dec 19  2023 16S_flash.hist
-rw-rw-r-- 1 root root 1.4K Dec 19  2023 16S_flash.histogram
-rw-rw-r-- 1 root root 1.1M Dec 19  2023 16S_merge.fq.gz
-rw-rw-r-- 1 root root 416K Dec 19  2023 16S_vsearch_merge.fq.gz
-rw-rw-r-- 1 root root  33K Dec 19  2023 16Snano_R1.fq.gz
-rw-rw-r-- 1 root root  38K Dec 19  2023 16Snano_R2.fq.gz
-rw-rw-r-- 1 root root  233 Dec 19  2023 art_R1.fq.gz
-rw-rw-r-- 1 root root  236 Dec 19  2023 art_R2.fq.gz
-rw-rw-r-- 1 root root  299 Dec 19  2023 artificial.fa.gz
-rw-rw-r-- 1 root root  333 Dec 19  2023 artificial.fq.gz
-rw-rw-r-- 1 root root 273K Dec 19  2023 its-merge.fq.gz
-rw-rw-r-- 1 root root 355K Dec 19  2023 its_R1.fq.gz
-rw-rw-r-- 1 root root 500K Dec 19  2023 its_R2.fq.gz
-rw-rw-r-- 1 root root 328K Dec 19  2023 itsfilt_R1.fq.gz
-rw-rw-r-- 1 root root 440K Dec 19  2023 itsfilt_R2.fq.gz
-rw-rw-r-- 1 root root 2.1K Dec 19  2023 pico_R1.fq.gz
-rw-rw-r-- 1 root root 2.3K Dec 19  2023 pico_R2.fq.gz
-rw-rw-r-- 1 root root  33K Dec 19  2023 se.fq.gz
-rw-rw-r-- 1 root root 1011 Dec 19  2023 small.fq
OK: Checked INVALID directory line error count (got 2 expected 2)
OK: Checked valid directory SEQFU_TMPDIR_nevlh5 exit status (expected 0, got 0)
OK: Checked valid directory line count SEQFU_TMPDIR_nevlh5/out (got 1 expected 1)
OK: Checked valid directory line error count (got 0 expected 0)
FAIL: Finished with 23 passed, 1 failed

[erinyoung]

@taylorpaisie , if you're okay with my changes, we can deploy this image to dockerhub and quay

[taylorpaisie]

@erinyoung looks good to me! Thanks for all your advice and help, it's really helping me get better and learn more about building docker containers!

[erinyoung]

Perfect!

I'm going to

1. merge this PR
2. deploy a 'seqfu' image to staphb's dockerhub and quay repositories
3. use both tags of '1.20.3' and 'latest'

[erinyoung]

Thank you for putting this together!

You can check the status of the deploy here : https://github.com/StaPH-B/docker-builds/actions/runs/11184872785