From cae936b2edc4360e1fe13288b4db8b4a449b6d1d Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 22 Oct 2024 12:18:55 +1300 Subject: [PATCH] Updated BRAKER --- modules/gallvp/braker3/main.nf | 2 +- modules/nf-core/fastp/tests/main.nf.test.snap | 72 +++++++++---------- .../tests/main.nf.test.snap | 48 ++++++------- 3 files changed, 61 insertions(+), 61 deletions(-) diff --git a/modules/gallvp/braker3/main.nf b/modules/gallvp/braker3/main.nf index 3cba6f8..1826684 100644 --- a/modules/gallvp/braker3/main.nf +++ b/modules/gallvp/braker3/main.nf @@ -38,7 +38,7 @@ process BRAKER3 { cp -r \$AUGUSTUS_CONFIG_PATH \\ augustus_config - chmod -R a+w \\ + chmod -R a+x,a+r,a+w \\ augustus_config perl -p -e 's/^(>\\S+).*\$/\$1/' \\ diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap index 54be7e4..8135ae8 100644 --- a/modules/nf-core/fastp/tests/main.nf.test.snap +++ b/modules/nf-core/fastp/tests/main.nf.test.snap @@ -96,7 +96,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" + "test.fastp.json:md5,63273f642b5a4495ce7ccba2d4419edf" ] ], [ @@ -122,10 +122,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:43:28.665779" + "timestamp": "2024-10-22T12:06:55.738001" }, "test_fastp_paired_end_merged_adapterlist": { "content": [ @@ -135,7 +135,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,5914ca3f21ce162123a824e33e8564f6" + "test.fastp.json:md5,7412a2cca178cc149757b229d2730d24" ] ], [ @@ -167,10 +167,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:44:18.210375" + "timestamp": "2024-10-22T12:07:21.185385" }, "test_fastp_single_end_qc_only": { "content": [ @@ -180,7 +180,7 @@ "id": "test", "single_end": true }, - "test.fastp.json:md5,5cc5f01e449309e0e689ed6f51a2294a" + "test.fastp.json:md5,8117ddbdb1ae856821eb66f40b14ba05" ] ], [ @@ -206,10 +206,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:44:27.380974" + "timestamp": "2024-10-22T12:07:25.750015" }, "test_fastp_paired_end_trim_fail": { "content": [ @@ -247,7 +247,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,4c3268ddb50ea5b33125984776aa3519" + "test.fastp.json:md5,5b7664268c0537423ffaa162701dae70" ] ], [ @@ -255,10 +255,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:43:58.749589" + "timestamp": "2024-10-22T12:07:11.053249" }, "fastp - stub test_fastp_interleaved": { "content": [ @@ -708,7 +708,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,b712fd68ed0322f4bec49ff2a5237fcc" + "test.fastp.json:md5,defba10ab9bb3e4235a86d90a51a2e79" ] ], [ @@ -740,10 +740,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:44:08.68476" + "timestamp": "2024-10-22T12:07:15.879392" }, "test_fastp_paired_end - stub": { "content": [ @@ -860,7 +860,7 @@ "id": "test", "single_end": true }, - "test.fastp.json:md5,c852d7a6dba5819e4ac8d9673bedcacc" + "test.fastp.json:md5,898dafe80449209d752985698a8cded0" ] ], [ @@ -883,10 +883,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:43:18.834322" + "timestamp": "2024-10-22T12:06:50.404111" }, "test_fastp_single_end_trim_fail - stub": { "content": [ @@ -1145,7 +1145,7 @@ "id": "test", "single_end": true }, - "test.fastp.json:md5,b24e0624df5cc0b11cd5ba21b726fb22" + "test.fastp.json:md5,d09c3ec938c4a7bd04bd6398f42fa9ca" ] ], [ @@ -1153,10 +1153,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:43:38.910832" + "timestamp": "2024-10-22T12:07:01.115181" }, "test_fastp_single_end_trim_fail": { "content": [ @@ -1166,7 +1166,7 @@ "id": "test", "single_end": true }, - "test.fastp.json:md5,9a7ee180f000e8d00c7fb67f06293eb5" + "test.fastp.json:md5,4415a44b64ff54a7a450b0acec32bc46" ] ], [ @@ -1195,10 +1195,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:43:48.22378" + "timestamp": "2024-10-22T12:07:06.065606" }, "test_fastp_paired_end_qc_only": { "content": [ @@ -1208,7 +1208,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,623064a45912dac6f2b64e3f2e9901df" + "test.fastp.json:md5,6ad01e6f6a98daf02410273af0b8ecea" ] ], [ @@ -1234,10 +1234,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:44:36.334938" + "timestamp": "2024-10-22T12:07:30.542067" }, "test_fastp_paired_end_qc_only - stub": { "content": [ diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap index e7d1f51..5eafe55 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap @@ -28,7 +28,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" + "test.fastp.json:md5,63273f642b5a4495ce7ccba2d4419edf" ] ], [ @@ -55,9 +55,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:56:01.933832" + "timestamp": "2024-10-22T12:08:27.512432" }, "save_trimmed_fail": { "content": [ @@ -88,7 +88,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,4c3268ddb50ea5b33125984776aa3519" + "test.fastp.json:md5,5b7664268c0537423ffaa162701dae70" ] ], [ @@ -127,9 +127,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:57:38.736" + "timestamp": "2024-10-22T12:09:27.209243" }, "skip_umi_extract": { "content": [ @@ -160,7 +160,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" + "test.fastp.json:md5,63273f642b5a4495ce7ccba2d4419edf" ] ], [ @@ -189,9 +189,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:56:47.905105" + "timestamp": "2024-10-22T12:08:55.436619" }, "umi_discard_read = 2": { "content": [ @@ -222,7 +222,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" + "test.fastp.json:md5,63273f642b5a4495ce7ccba2d4419edf" ] ], [ @@ -251,9 +251,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:57:05.436744" + "timestamp": "2024-10-22T12:09:07.272136" }, "umi_discard_read = 2 - stub": { "content": [ @@ -569,7 +569,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,b712fd68ed0322f4bec49ff2a5237fcc" + "test.fastp.json:md5,defba10ab9bb3e4235a86d90a51a2e79" ] ], [ @@ -604,9 +604,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:57:57.472342" + "timestamp": "2024-10-22T12:09:37.797126" }, "skip_trimming": { "content": [ @@ -668,7 +668,7 @@ "id": "test", "single_end": true }, - "test.fastp.json:md5,d39c5c6d9a2e35fb60d26ced46569af6" + "test.fastp.json:md5,b8dca1b3f56429748ab1ee6b84d9880a" ] ], [ @@ -695,9 +695,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:56:26.778625" + "timestamp": "2024-10-22T12:08:43.752347" }, "min_trimmed_reads = 26": { "content": [ @@ -728,7 +728,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,b712fd68ed0322f4bec49ff2a5237fcc" + "test.fastp.json:md5,defba10ab9bb3e4235a86d90a51a2e79" ] ], [ @@ -763,9 +763,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:58:16.36697" + "timestamp": "2024-10-22T12:09:48.309043" }, "min_trimmed_reads = 26 - stub": { "content": [ @@ -1676,7 +1676,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" + "test.fastp.json:md5,63273f642b5a4495ce7ccba2d4419edf" ] ], [ @@ -1705,9 +1705,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:55:50.614571" + "timestamp": "2024-10-22T12:08:22.300843" }, "sarscov2 paired-end [fastq] - stub": { "content": [