From aab189b26fe00c4882a8b3df6a2c772bcac0cccf Mon Sep 17 00:00:00 2001 From: "Davi Marcon (@mxrcon)" Date: Thu, 28 Apr 2022 14:41:41 -0300 Subject: [PATCH 1/4] fix on `fastqc` module and `qc_reports` workflow --- modules/qc/fastqc.nf | 2 +- workflows/qc_reports.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/qc/fastqc.nf b/modules/qc/fastqc.nf index cc00455..f4b0f60 100644 --- a/modules/qc/fastqc.nf +++ b/modules/qc/fastqc.nf @@ -7,7 +7,7 @@ process FASTQC { output: tuple path('*.html'), path('*.zip') - + path("*.{html,zip}"), emit: MULTIQC script: diff --git a/workflows/qc_reports.nf b/workflows/qc_reports.nf index d4666ae..6d7048e 100644 --- a/workflows/qc_reports.nf +++ b/workflows/qc_reports.nf @@ -8,6 +8,6 @@ workflow QC_REPORTS { main: FASTQC(reads_ch) - MULTIQC(FASTQC.out.collect()) + MULTIQC(FASTQC.out.MULTIQC.collect()) } From 41d081372a49d80beff681b7efd1115bbc99a782 Mon Sep 17 00:00:00 2001 From: "Davi Marcon (@mxrcon)" Date: Thu, 28 Apr 2022 14:49:03 -0300 Subject: [PATCH 2/4] updating multiqc version --- conda_envs/mtbseq-nf-env.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda_envs/mtbseq-nf-env.yml b/conda_envs/mtbseq-nf-env.yml index bd708ea..59087c4 100644 --- a/conda_envs/mtbseq-nf-env.yml +++ b/conda_envs/mtbseq-nf-env.yml @@ -6,4 +6,4 @@ dependencies: - bioconda::mtbseq=1.0.3 - bioconda/linux-64::gatk=3.8.0=py36_0 - bioconda::fastqc=0.11.9 - - bioconda::multiqc=1.9 + - bioconda::multiqc=1.12 From 3ae3f5db2921ff3a9c64056433290545b1876a43 Mon Sep 17 00:00:00 2001 From: Abhinav Sharma Date: Fri, 29 Apr 2022 14:00:44 +0200 Subject: [PATCH 3/4] Update workflows/qc_reports.nf --- workflows/qc_reports.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/qc_reports.nf b/workflows/qc_reports.nf index 6d7048e..b7d44ab 100644 --- a/workflows/qc_reports.nf +++ b/workflows/qc_reports.nf @@ -8,6 +8,6 @@ workflow QC_REPORTS { main: FASTQC(reads_ch) - MULTIQC(FASTQC.out.MULTIQC.collect()) + MULTIQC(FASTQC.out.html_zip_ch.collect()) } From af5175b1753a70681aecd04fee3322ddef89f460 Mon Sep 17 00:00:00 2001 From: Abhinav Sharma Date: Fri, 29 Apr 2022 14:00:49 +0200 Subject: [PATCH 4/4] Update modules/qc/fastqc.nf --- modules/qc/fastqc.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/qc/fastqc.nf b/modules/qc/fastqc.nf index f4b0f60..961bdb7 100644 --- a/modules/qc/fastqc.nf +++ b/modules/qc/fastqc.nf @@ -7,7 +7,7 @@ process FASTQC { output: tuple path('*.html'), path('*.zip') - path("*.{html,zip}"), emit: MULTIQC + path("*.{html,zip}"), emit: html_zip_ch script: