diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index cb74c549010d..4d1f9dd43ff7 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,8 +1,10 @@ name: tabix_tabix + channels: - conda-forge - bioconda - defaults + dependencies: - - bioconda::tabix=1.11 - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 532b558eff5e..b5c38a786389 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -36,8 +36,8 @@ process TABIX_TABIX { """ touch ${tab}.tbi touch ${tab}.csi + cat <<-END_VERSIONS > versions.yml - "${task.process}": tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test index 3a150c708fbe..38fbdfdd34fe 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test @@ -25,11 +25,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.tbi[0][1]).name - ).match("tbi_bed") - } + process.out, + file(process.out.tbi[0][1]).name + ).match() } ) } } @@ -50,11 +49,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.tbi[0][1]).name - ).match("tbi_gff") - } + process.out, + file(process.out.tbi[0][1]).name).match() } ) } @@ -76,11 +73,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.tbi[0][1]).name - ).match("tbi_vcf") - } + process.out, + file(process.out.tbi[0][1]).name + ).match() } ) } @@ -102,11 +98,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.csi[0][1]).name - ).match("vcf_csi") - } + process.out, + file(process.out.csi[0][1]).name + ).match() } ) } @@ -129,11 +124,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.csi[0][1]).name - ).match("vcf_csi_stub") - } + process.out, + file(process.out.csi[0][1]).name + ).match() } ) } diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap index 77b3bb056a97..c2b9ed0b8005 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap @@ -1,24 +1,4 @@ { - "vcf_csi_stub": { - "content": [ - "test.vcf.gz.csi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-03-04T14:51:59.788002" - }, - "tbi_gff": { - "content": [ - "genome.gff3.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-02-19T14:53:37.420216" - }, "sarscov2_gff_tbi": { "content": [ { @@ -50,13 +30,14 @@ "versions": [ "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } + }, + "genome.gff3.gz.tbi" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-19T11:30:08.097194659" + "timestamp": "2024-07-19T12:06:25.653807564" }, "sarscov2_bedgz_tbi": { "content": [ @@ -89,33 +70,14 @@ "versions": [ "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-19T11:29:56.691350166" - }, - "tbi_vcf": { - "content": [ - "test.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-02-19T14:53:46.402522" - }, - "vcf_csi": { - "content": [ - "test.vcf.gz.csi" + }, + "test.bed.gz.tbi" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-02-19T14:53:54.921189" + "timestamp": "2024-07-19T12:06:09.754082161" }, "sarscov2_vcf_tbi": { "content": [ @@ -148,13 +110,14 @@ "versions": [ "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } + }, + "test.vcf.gz.tbi" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-19T11:30:19.881620622" + "timestamp": "2024-07-19T12:06:40.042648294" }, "sarscov2_vcf_csi_stub": { "content": [ @@ -176,7 +139,7 @@ ] ], "2": [ - "versions.yml:md5,9f0a973d840bf1ff116773f51b89ac1b" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ], "csi": [ [ @@ -195,15 +158,16 @@ ] ], "versions": [ - "versions.yml:md5,9f0a973d840bf1ff116773f51b89ac1b" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } + }, + "test.vcf.gz.csi" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-19T11:30:42.00245281" + "timestamp": "2024-07-19T12:07:08.700367261" }, "sarscov2_vcf_csi": { "content": [ @@ -236,22 +200,13 @@ "versions": [ "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-19T11:30:31.015047391" - }, - "tbi_bed": { - "content": [ - "test.bed.gz.tbi" + }, + "test.vcf.gz.csi" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-02-19T14:53:28.947628" + "timestamp": "2024-07-19T12:06:55.362067748" } } \ No newline at end of file