From b7414764a542b1b5a0f2dc4a99641816837b95c6 Mon Sep 17 00:00:00 2001 From: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Date: Tue, 17 Mar 2026 16:02:39 -0300 Subject: [PATCH 1/3] Remove checkIfExists from interop file resolution --- subworkflows/nf-core/bcl_demultiplex/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/nf-core/bcl_demultiplex/main.nf b/subworkflows/nf-core/bcl_demultiplex/main.nf index 7061cfffbe18..5fed08bbe0f8 100644 --- a/subworkflows/nf-core/bcl_demultiplex/main.nf +++ b/subworkflows/nf-core/bcl_demultiplex/main.nf @@ -60,7 +60,7 @@ workflow BCL_DEMULTIPLEX { // MODULE: multiqcsav ch_mqcsav_input = ch_flowcell .map { meta, _samplesheet, flowcell -> - def interop = files(file(flowcell).resolve("InterOp/*.bin"), checkIfExists: true) + def interop = files(file(flowcell).resolve("InterOp/*.bin")) def xml = files(file(flowcell).resolve("*.xml"), checkIfExists: true) return [meta, xml, interop] } From 4045dfecee96674412e9ef4576735ab226923344 Mon Sep 17 00:00:00 2001 From: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Date: Wed, 18 Mar 2026 10:55:42 -0300 Subject: [PATCH 2/3] Fix interop file resolution for multiqcsav module --- subworkflows/nf-core/bcl_demultiplex/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/nf-core/bcl_demultiplex/main.nf b/subworkflows/nf-core/bcl_demultiplex/main.nf index 5fed08bbe0f8..09e4d2a07342 100644 --- a/subworkflows/nf-core/bcl_demultiplex/main.nf +++ b/subworkflows/nf-core/bcl_demultiplex/main.nf @@ -60,7 +60,8 @@ workflow BCL_DEMULTIPLEX { // MODULE: multiqcsav ch_mqcsav_input = ch_flowcell .map { meta, _samplesheet, flowcell -> - def interop = files(file(flowcell).resolve("InterOp/*.bin")) + def interopDir = file(flowcell).resolve("InterOp") + def interop = interopDir.exists() ? files("${interopDir}/*.bin") : [] def xml = files(file(flowcell).resolve("*.xml"), checkIfExists: true) return [meta, xml, interop] } From 20380872d53321eaf7415ae656f0c4f72ef0c9fb Mon Sep 17 00:00:00 2001 From: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Date: Wed, 18 Mar 2026 15:14:27 -0300 Subject: [PATCH 3/3] Fix interopDir existence check in main.nf --- subworkflows/nf-core/bcl_demultiplex/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/nf-core/bcl_demultiplex/main.nf b/subworkflows/nf-core/bcl_demultiplex/main.nf index 09e4d2a07342..08ae1585456b 100644 --- a/subworkflows/nf-core/bcl_demultiplex/main.nf +++ b/subworkflows/nf-core/bcl_demultiplex/main.nf @@ -61,7 +61,7 @@ workflow BCL_DEMULTIPLEX { ch_mqcsav_input = ch_flowcell .map { meta, _samplesheet, flowcell -> def interopDir = file(flowcell).resolve("InterOp") - def interop = interopDir.exists() ? files("${interopDir}/*.bin") : [] + def interop = file(interopDir).exists() ? files("${interopDir}/*.bin") : [] def xml = files(file(flowcell).resolve("*.xml"), checkIfExists: true) return [meta, xml, interop] }