diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff index e2f8a54..ad5b6fe 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff +++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff @@ -41,7 +41,7 @@ Changes in 'fastqscreen/fastqscreen/main.nf': output: tuple val(meta), path("*.txt") , emit: txt -@@ -24,13 +24,18 @@ +@@ -24,13 +24,22 @@ script: def prefix = task.ext.prefix ?: "${meta.id}" def args = task.ext.args ?: "" @@ -62,6 +62,10 @@ Changes in 'fastqscreen/fastqscreen/main.nf': $reads \\ - $args \\ + $args ++ ++ mv *_screen.txt ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.txt ++ mv *_screen.html ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.html ++ mv *_screen.png ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.png cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf index 5037db6..c0f98b9 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/main.nf +++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf @@ -37,6 +37,10 @@ process FASTQSCREEN_FASTQSCREEN { $reads \\ $args + mv *_screen.txt ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.txt + mv *_screen.html ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.html + mv *_screen.png ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.png + cat <<-END_VERSIONS > versions.yml "${task.process}": fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//') diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap index 0e8fec2..9207f88 100644 --- a/tests/MiSeq.main.nf.test.snap +++ b/tests/MiSeq.main.nf.test.snap @@ -4,12 +4,12 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8", "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf", - "multiqc_fastq_screen.txt:md5,88473b5190a4ff3bbe5a1b5b92da2601" + "multiqc_fastq_screen.txt:md5,435d8c1ac6e237448c9ce38e853ac82e" ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T13:33:59.180570696" + "timestamp": "2024-11-14T11:21:34.348023" } } \ No newline at end of file diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap index c22361f..8b0f136 100644 --- a/tests/NovaSeq6000.main.nf.test.snap +++ b/tests/NovaSeq6000.main.nf.test.snap @@ -4,28 +4,28 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d", "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732", - "multiqc_fastq_screen.txt:md5,836b01175da79f0de458df899b9751e1", + "multiqc_fastq_screen.txt:md5,c7b24e20fd157128924384e52eb3405d", "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78", "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921", - "multiqc_fastq_screen.txt:md5,fd72aaf00fd4fac3da4ef222608e0c32", + "multiqc_fastq_screen.txt:md5,a1e15006994d06a47634ccf07a08df0f", "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f", "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148", - "multiqc_fastq_screen.txt:md5,301fe12a6c6ccd09904c4f759008d416", + "multiqc_fastq_screen.txt:md5,d4f1cc5396c4f719b1fcaab2470e7d7c", "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347", "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c", - "multiqc_fastq_screen.txt:md5,045f5b7623f6abb99b7075734fdb0cf4", + "multiqc_fastq_screen.txt:md5,02246ddb4bf5373b157b45eab698cdc8", "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5", "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a", - "multiqc_fastq_screen.txt:md5,ee786f054e356ee005ca33c7558866dc" + "multiqc_fastq_screen.txt:md5,483995ed26ba25b3217650840b2d82fa" ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T13:35:28.998292704" + "timestamp": "2024-11-14T11:22:20.902938" } } \ No newline at end of file diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap index b3407e2..da7ba9a 100644 --- a/tests/NovaSeq6000.main_subsample.nf.test.snap +++ b/tests/NovaSeq6000.main_subsample.nf.test.snap @@ -4,28 +4,28 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514", "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c", - "multiqc_fastq_screen.txt:md5,2730834c61a9e1349b357ef6a729ddd9", + "multiqc_fastq_screen.txt:md5,c7b24e20fd157128924384e52eb3405d", "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8", "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60", - "multiqc_fastq_screen.txt:md5,a2b7469ab6b81d2872214eeba32933f5", + "multiqc_fastq_screen.txt:md5,a1e15006994d06a47634ccf07a08df0f", "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab", "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f", - "multiqc_fastq_screen.txt:md5,956cb8876c334293186ea213c4c39c6e", + "multiqc_fastq_screen.txt:md5,d4f1cc5396c4f719b1fcaab2470e7d7c", "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b", "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be", - "multiqc_fastq_screen.txt:md5,81cedab716aa382d7b4db2e42b681cb2", + "multiqc_fastq_screen.txt:md5,02246ddb4bf5373b157b45eab698cdc8", "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f", "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012", - "multiqc_fastq_screen.txt:md5,8bbb1968587dbf3139bac07991a225cb" + "multiqc_fastq_screen.txt:md5,483995ed26ba25b3217650840b2d82fa" ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T13:36:43.785887669" + "timestamp": "2024-11-14T11:23:19.55095" } } \ No newline at end of file diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap index 17178fd..74c12f5 100644 --- a/tests/PromethION.main.nf.test.snap +++ b/tests/PromethION.main.nf.test.snap @@ -4,12 +4,12 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0", "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32", - "multiqc_fastq_screen.txt:md5,37efa56cefb899abf506cf7a7fba0d54" + "multiqc_fastq_screen.txt:md5,2931dcec302d74c378b69a0831363224" ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T13:37:39.008847194" + "timestamp": "2024-11-14T11:23:42.382002" } } \ No newline at end of file