diff --git a/env/Dockerfile b/env/Dockerfile index 94c72a5..86d07a3 100644 --- a/env/Dockerfile +++ b/env/Dockerfile @@ -19,5 +19,3 @@ RUN conda update -y conda && \ WORKDIR "/opt" RUN wget https://github.com/seppinho/mutserve/releases/download/v2.0.0-rc13.lpa/mutserve_LPA_adapted.jar - - diff --git a/tests/lib/processes/cluster.nf.test b/tests/lib/processes/cluster.nf.test index 6183d70..f6091ca 100644 --- a/tests/lib/processes/cluster.nf.test +++ b/tests/lib/processes/cluster.nf.test @@ -17,7 +17,7 @@ nextflow_process { ["barcode06", "raw", "$baseDir/tests/input/cluster/barcode06/detected_umis.fastq"], ["barcode07", "raw", "$baseDir/tests/input/cluster/barcode07/detected_umis.fastq"] ) - input[1] = Channel.of("raw", "raw", "raw", "raw", "raw", "raw") + input[1] ="raw" """ } } diff --git a/tests/lib/processes/detect_umi_fastq.nf.test b/tests/lib/processes/detect_umi_fastq.nf.test index 614389a..3b1ee23 100644 --- a/tests/lib/processes/detect_umi_fastq.nf.test +++ b/tests/lib/processes/detect_umi_fastq.nf.test @@ -15,7 +15,7 @@ nextflow_process { ["barcode04", "raw", "$baseDir/tests/input/detect_umi/barcode04/lpa2645_filtered.fastq"], ["barcode05", "raw", "$baseDir/tests/input/detect_umi/barcode05/lpa2645_filtered.fastq"], ) - input[1] = Channel.of("raw", "raw", "raw", "raw") + input[1] = "raw" input[2] = file("$baseDir/bin/extract_umis.py") """ } @@ -41,7 +41,7 @@ nextflow_process { ["barcode04", "raw", "$baseDir/tests/input/detect_umi/barcode04/lpa2645_filtered.fastq"], ["barcode05", "raw", "$baseDir/tests/input/detect_umi/barcode05/lpa2645_filtered.fastq"], ) - input[1] = Channel.of("raw", "raw", "raw", "raw") + input[1] = "raw" input[2] = file("$baseDir/bin/extract_umis.py") """ } diff --git a/tests/lib/processes/freebayes.nf.test b/tests/lib/processes/freebayes.nf.test index 0822426..b37501b 100644 --- a/tests/lib/processes/freebayes.nf.test +++ b/tests/lib/processes/freebayes.nf.test @@ -14,7 +14,7 @@ nextflow_process { process { """ input[0] = Channel.of(["barcode03", "final", "$baseDir/tests/input/variant_calling/barcode03/final.bam", "$baseDir/tests/input/variant_calling/barcode03/final.bam.bai"]) - input[1] = Channel.of("final") + input[1] = "final" input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta") input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai") """ @@ -41,7 +41,7 @@ nextflow_process { ["barcode04", "final", "$baseDir/tests/input/variant_calling/barcode04/final.bam", "$baseDir/tests/input/variant_calling/barcode04/final.bam.bai"], ["barcode05", "final", "$baseDir/tests/input/variant_calling/barcode05/final.bam", "$baseDir/tests/input/variant_calling/barcode05/final.bam.bai"] ) - input[1] = Channel.of("final", "final", "final") + input[1] = "final" input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta") input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai") """ diff --git a/tests/lib/processes/freebayes.nf.test.snap b/tests/lib/processes/freebayes.nf.test.snap index 84c45d6..28c7712 100644 --- a/tests/lib/processes/freebayes.nf.test.snap +++ b/tests/lib/processes/freebayes.nf.test.snap @@ -3,14 +3,14 @@ "content": [ { "0": [ - "final.vcf:md5,88efc7556e75a4896acb25af4fd891ea", - "final.vcf:md5,8d2f225076db263df46ea74c3444d8a1", - "final.vcf:md5,c1ef037ccb4f791326fda68ef02ab497" + "final.vcf:md5,bf6dfb83c6e0762789976816b72af4e6", + "final.vcf:md5,c15c281e18b741734eb928f7112a02a4", + "final.vcf:md5,c9eb084d495bd1facf2a9049cb439c86" ], "variants": [ - "final.vcf:md5,88efc7556e75a4896acb25af4fd891ea", - "final.vcf:md5,8d2f225076db263df46ea74c3444d8a1", - "final.vcf:md5,c1ef037ccb4f791326fda68ef02ab497" + "final.vcf:md5,bf6dfb83c6e0762789976816b72af4e6", + "final.vcf:md5,c15c281e18b741734eb928f7112a02a4", + "final.vcf:md5,c9eb084d495bd1facf2a9049cb439c86" ] } ], @@ -18,16 +18,16 @@ "nf-test": "0.8.4", "nextflow": "23.10.0" }, - "timestamp": "2024-03-11T12:43:44.072561" + "timestamp": "2024-06-18T12:20:32.632422" }, "Should run without failures": { "content": [ { "0": [ - "final.vcf:md5,c1ef037ccb4f791326fda68ef02ab497" + "final.vcf:md5,c9eb084d495bd1facf2a9049cb439c86" ], "variants": [ - "final.vcf:md5,c1ef037ccb4f791326fda68ef02ab497" + "final.vcf:md5,c9eb084d495bd1facf2a9049cb439c86" ] } ], @@ -35,6 +35,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.0" }, - "timestamp": "2024-03-11T12:43:32.975611" + "timestamp": "2024-06-18T12:20:22.431414" } } \ No newline at end of file diff --git a/tests/lib/processes/lofreq.nf.test b/tests/lib/processes/lofreq.nf.test index 1b06613..34f3c33 100644 --- a/tests/lib/processes/lofreq.nf.test +++ b/tests/lib/processes/lofreq.nf.test @@ -14,7 +14,7 @@ nextflow_process { process { """ input[0] = Channel.of(["barcode03", "final", "$baseDir/tests/input/variant_calling/barcode03/final.bam", "$baseDir/tests/input/variant_calling/barcode03/final.bam.bai"]) - input[1] = Channel.of("final") + input[1] = "final" input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta") input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai") """ @@ -41,7 +41,7 @@ nextflow_process { ["barcode04", "final", "$baseDir/tests/input/variant_calling/barcode04/final.bam", "$baseDir/tests/input/variant_calling/barcode04/final.bam.bai"], ["barcode05", "final", "$baseDir/tests/input/variant_calling/barcode05/final.bam", "$baseDir/tests/input/variant_calling/barcode05/final.bam.bai"] ) - input[1] = Channel.of("final", "final", "final") + input[1] = "final" input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta") input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai") """ diff --git a/tests/lib/processes/lofreq.nf.test.snap b/tests/lib/processes/lofreq.nf.test.snap index 08d5dde..4f43016 100644 --- a/tests/lib/processes/lofreq.nf.test.snap +++ b/tests/lib/processes/lofreq.nf.test.snap @@ -3,14 +3,14 @@ "content": [ { "0": [ - "final.vcf:md5,1834d639e6fd638fb43dc15430b2c507", - "final.vcf:md5,527bcb8a79c99a9cf4deb47b54b0d068", - "final.vcf:md5,7d03b1b5af994b65dce89c71f09771b3" + "final.vcf:md5,13437d43022bd6b7a171daed88c010c4", + "final.vcf:md5,1b57a477112f541443d246db37138216", + "final.vcf:md5,810ba2f38eb3bda15699654945daa21a" ], "variants": [ - "final.vcf:md5,1834d639e6fd638fb43dc15430b2c507", - "final.vcf:md5,527bcb8a79c99a9cf4deb47b54b0d068", - "final.vcf:md5,7d03b1b5af994b65dce89c71f09771b3" + "final.vcf:md5,13437d43022bd6b7a171daed88c010c4", + "final.vcf:md5,1b57a477112f541443d246db37138216", + "final.vcf:md5,810ba2f38eb3bda15699654945daa21a" ] } ], @@ -18,16 +18,16 @@ "nf-test": "0.8.4", "nextflow": "23.10.0" }, - "timestamp": "2024-03-11T15:08:10.610508" + "timestamp": "2024-06-18T12:20:15.213263" }, "Should run without failures": { "content": [ { "0": [ - "final.vcf:md5,1834d639e6fd638fb43dc15430b2c507" + "final.vcf:md5,13437d43022bd6b7a171daed88c010c4" ], "variants": [ - "final.vcf:md5,1834d639e6fd638fb43dc15430b2c507" + "final.vcf:md5,13437d43022bd6b7a171daed88c010c4" ] } ], @@ -35,6 +35,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.0" }, - "timestamp": "2024-03-11T15:07:59.738964" + "timestamp": "2024-06-18T12:20:05.981639" } } \ No newline at end of file diff --git a/tests/lib/processes/map_reads.nf.test b/tests/lib/processes/map_reads.nf.test index fc954da..40b6dc5 100644 --- a/tests/lib/processes/map_reads.nf.test +++ b/tests/lib/processes/map_reads.nf.test @@ -14,7 +14,7 @@ nextflow_process { ["barcode04", "raw", "$baseDir/tests/input/mapping/barcode04/raw/lpa2645_filtered.fastq"], ["barcode05", "raw", "$baseDir/tests/input/mapping/barcode05/raw/lpa2645_filtered.fastq"], ) - input[1] = Channel.from("raw", "raw", "raw") + input[1] = "raw" input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta") """ } @@ -37,7 +37,7 @@ nextflow_process { ["barcode04", "consensus", "$baseDir/tests/input/mapping/barcode04/consensus/masked_consensus.fastq"], ["barcode05", "consensus", "$baseDir/tests/input/mapping/barcode05/consensus/masked_consensus.fastq"], ) - input[1] = Channel.from("consensus", "consensus", "consensus") + input[1] = "consensus" input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta") """ } @@ -60,7 +60,7 @@ nextflow_process { ["barcode04", "final", "$baseDir/tests/input/mapping/barcode04/final/final.fastq"], ["barcode05", "final", "$baseDir/tests/input/mapping/barcode05/final/final.fastq"], ) - input[1] = Channel.from("final", "final", "final") + input[1] = "final" input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta") """ } diff --git a/tests/lib/processes/mutserve.nf.test b/tests/lib/processes/mutserve.nf.test index 3611cb5..68f5589 100644 --- a/tests/lib/processes/mutserve.nf.test +++ b/tests/lib/processes/mutserve.nf.test @@ -14,7 +14,7 @@ nextflow_process { process { """ input[0] = Channel.of(["barcode03", "final", "$baseDir/tests/input/variant_calling/barcode03/final.bam", "$baseDir/tests/input/variant_calling/barcode03/final.bam.bai"]) - input[1] = Channel.of("final") + input[1] = "final" input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.bed") input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta") input[4] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai") @@ -42,7 +42,7 @@ nextflow_process { ["barcode04", "final", "$baseDir/tests/input/variant_calling/barcode04/final.bam", "$baseDir/tests/input/variant_calling/barcode04/final.bam.bai"], ["barcode05", "final", "$baseDir/tests/input/variant_calling/barcode05/final.bam", "$baseDir/tests/input/variant_calling/barcode05/final.bam.bai"] ) - input[1] = Channel.of("final", "final", "final") + input[1] = "final" input[2] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.bed") input[3] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta") input[4] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai") diff --git a/tests/lib/processes/polish_cluster.nf.test b/tests/lib/processes/polish_cluster.nf.test index b942594..1760dd2 100644 --- a/tests/lib/processes/polish_cluster.nf.test +++ b/tests/lib/processes/polish_cluster.nf.test @@ -41,7 +41,7 @@ nextflow_process { process { """ input[0] = REFORMAT_FILTER_CLUSTER.out.smolecule_cluster_fastqs.transpose() - input[1] = Channel.of("consensus", "consensus", "consensus", "consensus", "consensus") + input[1] = "Consensus" """ } } diff --git a/tests/lib/processes/polish_cluster.nf.test.snap b/tests/lib/processes/polish_cluster.nf.test.snap index 6e759d0..54e777c 100644 --- a/tests/lib/processes/polish_cluster.nf.test.snap +++ b/tests/lib/processes/polish_cluster.nf.test.snap @@ -27,33 +27,1113 @@ "barcode03", "raw", "smolecule4sub0_consensus.fastq:md5,813d3d07a2fe5a8ca343f758831208fd" - ] - ], - "consensus_fastq": [ + ], [ "barcode03", "raw", + "smolecule5sub0_consensus.fastq:md5,3b72bf249e00402e6b78910ac50cd90c" + ], + [ + "barcode04", + "raw", + "smolecule0sub0_consensus.fastq:md5,f17be012ddb9d4f29901cc32fb322aaa" + ], + [ + "barcode04", + "raw", + "smolecule1sub0_consensus.fastq:md5,ca4938fd91ca380538cd84264577c03b" + ], + [ + "barcode04", + "raw", + "smolecule2sub0_consensus.fastq:md5,8a36b1d569dadfb78a4b50e4417f1d52" + ], + [ + "barcode04", + "raw", + "smolecule3sub0_consensus.fastq:md5,c685c4676c25dd1b48a0734984376b0c" + ], + [ + "barcode04", + "raw", + "smolecule4sub0_consensus.fastq:md5,294e15ca0e9d5a2e3708e88cced55e7c" + ], + [ + "barcode04", + "raw", + "smolecule5sub0_consensus.fastq:md5,68f64fa2851c4739c5b3f134430a6ca2" + ], + [ + "barcode05", + "raw", "smolecule0sub0_consensus.fastq:md5,85c055b607a0ae893d1e8d2c0fe298af" ], [ - "barcode03", + "barcode05", "raw", - "smolecule1sub0_consensus.fastq:md5,0390b95558912435618e9a0569280a8f" + "smolecule10sub0_consensus.fastq:md5,50a974f20f8a3f4b7fe1cbce51792b34" ], [ - "barcode03", + "barcode05", "raw", - "smolecule2sub0_consensus.fastq:md5,0ef3b301741224bf4aad61b61d6eb7c2" + "smolecule11sub0_consensus.fastq:md5,f7e5643d246b7eca963f00b15f0b43e2" ], [ - "barcode03", + "barcode05", "raw", - "smolecule3sub0_consensus.fastq:md5,7f4723552bfdd42432b6fb52d4483f56" + "smolecule1sub0_consensus.fastq:md5,29e295a2381fab938e3f4f745f0cf228" ], [ - "barcode03", + "barcode05", "raw", - "smolecule4sub0_consensus.fastq:md5,813d3d07a2fe5a8ca343f758831208fd" + "smolecule2sub0_consensus.fastq:md5,1f45048e1ec557b632ae71e2a6b2dfc7" + ], + [ + "barcode05", + "raw", + "smolecule3sub0_consensus.fastq:md5,0d696bc1323e65539b67d88793cdb5af" + ], + [ + "barcode05", + "raw", + "smolecule4sub0_consensus.fastq:md5,923ee827fc8b88cd58afb305d19cf0ad" + ], + [ + "barcode05", + "raw", + "smolecule5sub0_consensus.fastq:md5,0253f0d9d08498372fdd11a9917b3315" + ], + [ + "barcode05", + "raw", + "smolecule6sub0_consensus.fastq:md5,3994a65a83144473bdc65c8aa2c211be" + ], + [ + "barcode05", + "raw", + "smolecule7sub0_consensus.fastq:md5,97dd3f98778b3e4d4dd63dc18683af6c" + ], + [ + "barcode05", + "raw", + "smolecule8sub0_consensus.fastq:md5,10863a74f83c967093efdc8939e1a626" + ], + [ + "barcode05", + "raw", + "smolecule9sub0_consensus.fastq:md5,7d33c9a6f3fdd1d96521a28710f27acf" + ], + [ + "barcode06", + "raw", + "smolecule697sub0_consensus.fastq:md5,a6ab25dd5495ffb767ecfde466508f5a" + ], + [ + "barcode07", + "raw", + "smolecule101sub0_consensus.fastq:md5,4181c3a324659ee638f76025d59b2462" + ], + [ + "barcode07", + "raw", + "smolecule106sub0_consensus.fastq:md5,e8e5ede5883ca3d1ef165e3dbde54637" + ], + [ + "barcode07", + "raw", + "smolecule107sub0_consensus.fastq:md5,9fd7d556f4663e5bd7be9615a034bb37" + ], + [ + "barcode07", + "raw", + "smolecule109sub0_consensus.fastq:md5,50c0c2d59e7f1d65b54d37996e059ae3" + ], + [ + "barcode07", + "raw", + "smolecule10sub0_consensus.fastq:md5,c68fbb62fd9d78a89e433dbd17f52be0" + ], + [ + "barcode07", + "raw", + "smolecule113sub0_consensus.fastq:md5,a46b958f38569c29a55ec5e715bbf963" + ], + [ + "barcode07", + "raw", + "smolecule116sub0_consensus.fastq:md5,511003cb6dd833f2528784315d9392cc" + ], + [ + "barcode07", + "raw", + "smolecule116sub1_consensus.fastq:md5,9bfce1d635f111d6967441054e828c57" + ], + [ + "barcode07", + "raw", + "smolecule117sub0_consensus.fastq:md5,07fd23ca9b918030111b5af2277b65ca" + ], + [ + "barcode07", + "raw", + "smolecule119sub0_consensus.fastq:md5,805db200db813799ecbb3da7c0f84d29" + ], + [ + "barcode07", + "raw", + "smolecule124sub1_consensus.fastq:md5,5a360f2ec6e0c37aadf0d6faa53bd9ea" + ], + [ + "barcode07", + "raw", + "smolecule129sub1_consensus.fastq:md5,e470be349111e96077891ea1e4eea376" + ], + [ + "barcode07", + "raw", + "smolecule12sub2_consensus.fastq:md5,9c2d4270dcddcf363834416ffde1566d" + ], + [ + "barcode07", + "raw", + "smolecule132sub0_consensus.fastq:md5,6dd2310e60ad61258b8b5d43e4cc30c4" + ], + [ + "barcode07", + "raw", + "smolecule133sub0_consensus.fastq:md5,5766785b2e6dab648c7fd40c82eb596e" + ], + [ + "barcode07", + "raw", + "smolecule137sub0_consensus.fastq:md5,a44be9ab8baac61eb17f855d1c6f02e3" + ], + [ + "barcode07", + "raw", + "smolecule13sub0_consensus.fastq:md5,bd5f48cc95f8686877d1cd778edd0ab6" + ], + [ + "barcode07", + "raw", + "smolecule141sub0_consensus.fastq:md5,5c6f09a294f2b184755b8afc916c6b0f" + ], + [ + "barcode07", + "raw", + "smolecule145sub0_consensus.fastq:md5,51a1c865759c1ae082f8bc86eb37faba" + ], + [ + "barcode07", + "raw", + "smolecule149sub0_consensus.fastq:md5,787f32d94ce04ffba3d43e9e58a40f63" + ], + [ + "barcode07", + "raw", + "smolecule14sub0_consensus.fastq:md5,19450c65845598b6920b95fdea6cac8c" + ], + [ + "barcode07", + "raw", + "smolecule153sub1_consensus.fastq:md5,fbba202fb0cac609004a4a6201ce1685" + ], + [ + "barcode07", + "raw", + "smolecule155sub1_consensus.fastq:md5,2818f7f21da18a4fde960a8e0a97e8de" + ], + [ + "barcode07", + "raw", + 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"smolecule4sub1_consensus.fastq:md5,8207a1fb200c4ccc9100e578c679968d" + ], + [ + "barcode07", + "raw", + "smolecule50sub0_consensus.fastq:md5,8940dfdbb43471fb4bc52ed8ad09ffa6" + ], + [ + "barcode07", + "raw", + "smolecule51sub0_consensus.fastq:md5,7a04caa0b0d2762f0f99cbaed6725698" + ], + [ + "barcode07", + "raw", + "smolecule52sub1_consensus.fastq:md5,33957428f3ddd5bbb9db96099d6b2c10" + ], + [ + "barcode07", + "raw", + "smolecule53sub0_consensus.fastq:md5,f152fe2a618f8843916bf52f5cde5ff8" + ], + [ + "barcode07", + "raw", + "smolecule54sub1_consensus.fastq:md5,def604ae43d716f0382ef923b13c26b5" + ], + [ + "barcode07", + "raw", + "smolecule56sub0_consensus.fastq:md5,2f3eea6c003a4dc3e6ea692720d0c444" + ], + [ + "barcode07", + "raw", + "smolecule57sub0_consensus.fastq:md5,1d6def5c26e9232ea49526748b0e4f9e" + ], + [ + "barcode07", + "raw", + "smolecule5sub1_consensus.fastq:md5,2a84bd4895e01d284a4507dc63c85e42" + ], + [ + "barcode07", + "raw", + "smolecule60sub0_consensus.fastq:md5,2eef3b3bc2aa00c5baa8aa7477a6271d" + ], + [ + "barcode07", + "raw", + "smolecule61sub0_consensus.fastq:md5,4ea8937e5d621409a2983f945a6a186e" + ], + [ + "barcode07", + "raw", + "smolecule62sub0_consensus.fastq:md5,8d53046aec2deb3926c76ddc0b8df3ba" + ], + [ + "barcode07", + "raw", + "smolecule63sub0_consensus.fastq:md5,6874de4528d5b42cc518f6190d0fee6e" + ], + [ + "barcode07", + "raw", + "smolecule67sub0_consensus.fastq:md5,189858435a49fced49fb985a0f35c9e7" + ], + [ + "barcode07", + "raw", + "smolecule6sub2_consensus.fastq:md5,6e8507644d1b20ee2d9c34b66ca00a65" + ], + [ + "barcode07", + "raw", + "smolecule73sub0_consensus.fastq:md5,c98c2221c5ac87ccc880fd2174809297" + ], + [ + "barcode07", + "raw", + "smolecule74sub0_consensus.fastq:md5,816616d679b5a6112d65b55e21f88adb" + ], + [ + "barcode07", + "raw", + "smolecule77sub0_consensus.fastq:md5,7f018bcc964c4d4776c8366a3b010746" + ], + [ + "barcode07", + "raw", + "smolecule79sub1_consensus.fastq:md5,ab9f8623217cfe3abbc91c37a32d5c76" + ], + [ + "barcode07", + "raw", + "smolecule84sub0_consensus.fastq:md5,ad9e24dc14b18c0bffb01fa39a99289c" + ], + [ + "barcode07", + "raw", + "smolecule87sub0_consensus.fastq:md5,68fbea03ea8df614287dbceb5f94d5f0" + ], + [ + "barcode07", + "raw", + "smolecule89sub0_consensus.fastq:md5,aaa1a5a1ff7205743138c354b40d0c31" + ], + [ + "barcode07", + "raw", + "smolecule95sub0_consensus.fastq:md5,4e5376307200d9c1b3fa6a6af8ea55e3" + ], + [ + "barcode07", + "raw", + "smolecule98sub0_consensus.fastq:md5,90a3251ec19e37d7e35b88c2d98bbcdf" + ], + [ + "barcode07", + "raw", + "smolecule9sub0_consensus.fastq:md5,b2e992f6736fc0304e76f951d4353f0d" ] ] } @@ -62,6 +1142,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.0" }, - "timestamp": "2024-03-15T13:07:01.670879" + "timestamp": "2024-06-18T13:50:27.948644" } } \ No newline at end of file diff --git a/tests/lib/processes/reformat_filter_cluster.nf.test b/tests/lib/processes/reformat_filter_cluster.nf.test index e186a40..b624211 100644 --- a/tests/lib/processes/reformat_filter_cluster.nf.test +++ b/tests/lib/processes/reformat_filter_cluster.nf.test @@ -16,7 +16,7 @@ nextflow_process { ["barcode06", "raw", "$baseDir/tests/input/cluster/barcode06/detected_umis.fastq"], ["barcode07", "raw", "$baseDir/tests/input/cluster/barcode07/detected_umis.fastq"] ) - input[1] = Channel.of("raw", "raw", "raw", "raw", "raw") + input[1] = "raw" """ } @@ -32,7 +32,7 @@ nextflow_process { process { """ input[0] = CLUSTER.out.cluster_fastas - input[1] = Channel.of("raw", "raw", "raw", "raw", "raw") + input[1] = "raw" input[2] = file("$baseDir/bin/parse_clusters.py") """ } diff --git a/tests/lib/processes/split_reads.nf.test b/tests/lib/processes/split_reads.nf.test index bfd63e9..aa4ac21 100644 --- a/tests/lib/processes/split_reads.nf.test +++ b/tests/lib/processes/split_reads.nf.test @@ -14,7 +14,7 @@ nextflow_process { ["barcode03", "raw", "$baseDir/tests/input/split_reads/barcode03/merged.bam", "$baseDir/tests/input/split_reads/barcode03/merged.bam.bai"] ) input[1] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.bed") - input[2] = Channel.of("raw", "raw") + input[2] = "raw" input[3] = file("$baseDir/bin/filter_reads.py") """ } @@ -37,7 +37,7 @@ nextflow_process { ["barcode05", "raw", "$baseDir/tests/input/split_reads/barcode05/merged.bam", "$baseDir/tests/input/split_reads/barcode05/merged.bam.bai"] ) input[1] = file("$baseDir/tests/input/pipeline/ref/lpa-ref2645.bed") - input[2] = Channel.of("raw", "raw") + input[2] = "raw" input[3] = file("$baseDir/bin/filter_reads.py") """ } diff --git a/tests/nextflow.config b/tests/nextflow.config index 4cd871f..8fe487f 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -7,6 +7,6 @@ process { withName: '.*' { cpus = 1 - memory = 1.GB + memory = 2.GB } } \ No newline at end of file