From 4031e6af90990fe14028ce7332d99aea096feffc Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Thu, 4 Apr 2024 10:17:01 +0000 Subject: [PATCH 01/11] First_commit --- .gitpod.yml | 2 ++ README.md | 6 ++++++ main.nf | 2 ++ nextflow.config | 2 ++ 4 files changed, 12 insertions(+) diff --git a/.gitpod.yml b/.gitpod.yml index cb19981..0783443 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,3 +1,5 @@ +image: nfcore/gitpod:latest + # List the start up tasks. Learn more https://www.gitpod.io/docs/config-start-tasks/ tasks: - name: Download Nextflow Tutorial diff --git a/README.md b/README.md index 9f5a3d0..c4afa9e 100755 --- a/README.md +++ b/README.md @@ -226,6 +226,12 @@ nextflow run main.nf -profile apptainer,local -resume \ nextflow run main.nf -profile docker,aws_batch -resume --input data/input_full-s3.csv --database "s3://pollen-metabarcoding-test-data/data/viridiplantae_all_2014.sintax.fa" --FW_primer "ATGCGATACTTGGTGTGAAT" --RV_primer "GCATATCAATAAGCGGAGGA" --custom_config /path/to/custom/config ``` +* Running on Gitpod: +If you wish to run on Gitpod, please be aware that the usearch (sintax_summary) module will fail, as Gitpod doesn't allow 32bit programs. +``` +nextflow run main.nf -profile docker,test_small -resume --gitpod +``` + ## Test Data The data used to test this pipeline via the [ENA ID: PRJEB26439](http://www.ebi.ac.uk/ena/data/view/PRJEB26439). There are two test profiles using this data: diff --git a/main.nf b/main.nf index 837077d..0386d14 100755 --- a/main.nf +++ b/main.nf @@ -68,8 +68,10 @@ workflow { VSEARCH_SINTAX(ch_sintax.fa, ch_sintax.db) ch_versions = ch_versions.mix(VSEARCH_SINTAX.out.versions.first()) + if (params.gitpod == null){ USEARCH_SINTAX_SUMMARY(VSEARCH_SINTAX.out.tsv) ch_versions = ch_versions.mix(USEARCH_SINTAX_SUMMARY.out.versions.first()) + } //Sometimes sintax produces different row lengths, only need first 2 CUTTING(VSEARCH_SINTAX.out.tsv) | R_PROCESSING diff --git a/nextflow.config b/nextflow.config index 51b1695..9ca520e 100755 --- a/nextflow.config +++ b/nextflow.config @@ -55,6 +55,8 @@ params { sintax_cutoff = null sintax_strand = null seed = 1312 + //gitpod + gitpod = null //defaults used by Eco-Flow when testing, overwrite on command-line with your own resources awsqueue = 'HUNDRED_QUEUE' awsregion = 'us-east-1' From 36a0f4976c6b07083d80e41ae9d4a25c7690a70d Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Thu, 4 Apr 2024 10:19:14 +0000 Subject: [PATCH 02/11] screen --- .gitpod.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitpod.yml b/.gitpod.yml index 0783443..b1ec78f 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -12,6 +12,7 @@ tasks: nextflow info unset JAVA_TOOL_OPTIONS echo 'Starting workspace !' + sudo apt-get update # List the ports to expose. Learn more https://www.gitpod.io/docs/config-ports/ ports: - port: 8000 \ No newline at end of file From 19840e3e56cb84bcb693ebe553aee2cc3c3d58d3 Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Thu, 4 Apr 2024 10:21:17 +0000 Subject: [PATCH 03/11] up --- .gitpod.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitpod.yml b/.gitpod.yml index b1ec78f..dbad8bb 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -12,7 +12,7 @@ tasks: nextflow info unset JAVA_TOOL_OPTIONS echo 'Starting workspace !' - sudo apt-get update + sudo apt-get screen # List the ports to expose. Learn more https://www.gitpod.io/docs/config-ports/ ports: - port: 8000 \ No newline at end of file From 41c1618eebc5602a37769bc2352dbda1178f5cab Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Thu, 4 Apr 2024 10:24:15 +0000 Subject: [PATCH 04/11] update --- .gitpod.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitpod.yml b/.gitpod.yml index dbad8bb..8ef98c5 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -12,7 +12,8 @@ tasks: nextflow info unset JAVA_TOOL_OPTIONS echo 'Starting workspace !' - sudo apt-get screen + sudo apt-get update + sudo apt-get -y install # List the ports to expose. Learn more https://www.gitpod.io/docs/config-ports/ ports: - port: 8000 \ No newline at end of file From 9d45c33bc259d8e83863348dc38a745c3b7f8923 Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Thu, 4 Apr 2024 10:25:48 +0000 Subject: [PATCH 05/11] screen_real --- .gitpod.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitpod.yml b/.gitpod.yml index 8ef98c5..07c0328 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -13,7 +13,7 @@ tasks: unset JAVA_TOOL_OPTIONS echo 'Starting workspace !' sudo apt-get update - sudo apt-get -y install + sudo apt-get -y screen # List the ports to expose. Learn more https://www.gitpod.io/docs/config-ports/ ports: - port: 8000 \ No newline at end of file From 6a006d633297771f786ab6787e8fe7dbd9c44035 Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Thu, 4 Apr 2024 10:27:04 +0000 Subject: [PATCH 06/11] screen --- .gitpod.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitpod.yml b/.gitpod.yml index 07c0328..e713fd7 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -13,7 +13,7 @@ tasks: unset JAVA_TOOL_OPTIONS echo 'Starting workspace !' sudo apt-get update - sudo apt-get -y screen + sudo apt-get install -y screen # List the ports to expose. Learn more https://www.gitpod.io/docs/config-ports/ ports: - port: 8000 \ No newline at end of file From 89c7c7116d81d3e6d2ca0efe598f4d4f081d3217 Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Thu, 4 Apr 2024 10:55:00 +0000 Subject: [PATCH 07/11] schema update --- nextflow_schema.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index 9bca27c..d3435ad 100755 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -187,6 +187,10 @@ "forks": { "type": "number", "description": "Maximum number of each process that will be run in parallel." + }, + "gitpod": { + "type": "string", + "description": "Skips usearch process, which does not run on gitpod (32bit)" } } }, From 13c0ca45be50804ea8d6a4cc6c350c90380e673c Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Thu, 4 Apr 2024 11:02:09 +0000 Subject: [PATCH 08/11] Fixed schema --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index d3435ad..e449500 100755 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -189,7 +189,7 @@ "description": "Maximum number of each process that will be run in parallel." }, "gitpod": { - "type": "string", + "type": "boolean", "description": "Skips usearch process, which does not run on gitpod (32bit)" } } From 334b70ee65f27e63de94058fff500e5da6d09cc6 Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Thu, 4 Apr 2024 12:40:01 +0000 Subject: [PATCH 09/11] fixed_test_r_processing --- tests/modules/local/r_processing.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/modules/local/r_processing.nf.test.snap b/tests/modules/local/r_processing.nf.test.snap index 723d6b1..96a5776 100644 --- a/tests/modules/local/r_processing.nf.test.snap +++ b/tests/modules/local/r_processing.nf.test.snap @@ -2,12 +2,12 @@ "r_processing": { "content": [ "ERR2537816.classified.tsv:md5,d7536874f239e304cca7667dc1ffde4d", - "summary.tsv:md5,4a575d1bc4bfb5f79cf160ae793e9c30" + "summary.tsv:md5,cdd728c2daee0aa13fcee439ff3460c2" ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-27T13:36:37.712309" + "timestamp": "2024-04-04T11:11:20.884715539" } } \ No newline at end of file From 94265865251609b69749708b503447dbbda4631a Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Thu, 4 Apr 2024 12:52:38 +0000 Subject: [PATCH 10/11] New snapshot vsearch sintax --- .../nf-core/vsearch/sintax/main.nf.test | 2 +- .../nf-core/vsearch/sintax/main.nf.test.snap | 37 +++++++++++++++++++ 2 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 tests/modules/nf-core/vsearch/sintax/main.nf.test.snap diff --git a/tests/modules/nf-core/vsearch/sintax/main.nf.test b/tests/modules/nf-core/vsearch/sintax/main.nf.test index 772563f..d4a7c28 100755 --- a/tests/modules/nf-core/vsearch/sintax/main.nf.test +++ b/tests/modules/nf-core/vsearch/sintax/main.nf.test @@ -27,7 +27,7 @@ nextflow_process { assert tsv[0].size() == 2 assert tsv[0][0].size() == 2 } - + assert snapshot(process.out).match() } } diff --git a/tests/modules/nf-core/vsearch/sintax/main.nf.test.snap b/tests/modules/nf-core/vsearch/sintax/main.nf.test.snap new file mode 100644 index 0000000..3cc0cab --- /dev/null +++ b/tests/modules/nf-core/vsearch/sintax/main.nf.test.snap @@ -0,0 +1,37 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "ERR2537816", + "single_end": false + }, + "ERR2537816.tsv:md5,84351a56e4ddf56df7403c9ffefa0f1b" + ] + ], + "1": [ + "versions.yml:md5,6584e256329124c6abe9e76715edfe92" + ], + "tsv": [ + [ + { + "id": "ERR2537816", + "single_end": false + }, + "ERR2537816.tsv:md5,84351a56e4ddf56df7403c9ffefa0f1b" + ] + ], + "versions": [ + "versions.yml:md5,6584e256329124c6abe9e76715edfe92" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-04T12:52:09.921597141" + } +} \ No newline at end of file From e19ae21904d1cdb20852a48b884aca4e6f52e47c Mon Sep 17 00:00:00 2001 From: chriswyatt1 Date: Fri, 5 Apr 2024 11:16:03 +0000 Subject: [PATCH 11/11] Fix snapshot cutadapt --- tests/modules/nf-core/cutadapt/main.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/modules/nf-core/cutadapt/main.nf.test.snap b/tests/modules/nf-core/cutadapt/main.nf.test.snap index 5a1d472..e27dfe4 100644 --- a/tests/modules/nf-core/cutadapt/main.nf.test.snap +++ b/tests/modules/nf-core/cutadapt/main.nf.test.snap @@ -1,13 +1,13 @@ { "cutadapt_fastqs": { "content": [ - "ERR2537816_1.trim.fastq.gz:md5,f9cb0dd1a4e2c3c871358d4d8dc7e490", - "ERR2537816_2.trim.fastq.gz:md5,c8333cd8e2f72a52122edf20ed159421" + "ERR2537816_1.trim.fastq.gz:md5,e9c82243f237a047eb2e095ed08da2f8", + "ERR2537816_2.trim.fastq.gz:md5,757f99993765c836965d6633bfbb5c97" ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-27T13:54:45.929629" + "timestamp": "2024-04-05T11:14:03.65794141" } } \ No newline at end of file