From daff863c8cdcbb0028725ec1bd97eb48bb3e0edc Mon Sep 17 00:00:00 2001
From: Marc Hoeppner <mphoeppner@gmail.com>
Date: Fri, 10 Jan 2025 07:26:18 +0100
Subject: [PATCH] Merging abricate databases per sample into one json

---
 assets/test/samples.csv                | 2 +-
 bin/gabi.py                            | 4 ++--
 modules/hamronization/abricate/main.nf | 8 ++++----
 nextflow.config                        | 2 +-
 subworkflows/amr_profiling/main.nf     | 2 +-
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/assets/test/samples.csv b/assets/test/samples.csv
index 691872d..2b22e3a 100644
--- a/assets/test/samples.csv
+++ b/assets/test/samples.csv
@@ -1,2 +1,2 @@
 sample_id,platform,single_end,R1,R2
-ERR1008684,ILLUMINA,false,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR100/004/ERR1008684/ERR1008684_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR100/004/ERR1008684/ERR1008684_2.fastq.gz
+SAMEA2707761,ILLUMINA,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR580/ERR580964/ERR580964_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR580/ERR580964/ERR580964_2.fastq.gz
diff --git a/bin/gabi.py b/bin/gabi.py
index 18ef7fc..669caa5 100755
--- a/bin/gabi.py
+++ b/bin/gabi.py
@@ -448,7 +448,7 @@ def main(yaml, template, output, reference, version, call, wd):
     if busco_data_all:
         # Draw the busco stats graph
         bdata = pd.DataFrame(data=busco_data_all, index=samples)
-        plot_labels = { "index": "Samples", "value": "Percentage"}
+        plot_labels = {"index": "Samples", "value": "Percentage"}
         h = len(samples)*25 if len(samples) > 10 else 300
         fig = px.bar(bdata, orientation='h', labels=plot_labels, height=h)
         data["Busco"] = fig.to_html(full_html=False)
@@ -559,4 +559,4 @@ def check_gc(refs, query):
 
 
 if __name__ == '__main__':
-    main(args.input, args.template, args.output, args.references, args.version, args.call, args.wd)
\ No newline at end of file
+    main(args.input, args.template, args.output, args.references, args.version, args.call, args.wd)
diff --git a/modules/hamronization/abricate/main.nf b/modules/hamronization/abricate/main.nf
index 186853d..09ede0d 100644
--- a/modules/hamronization/abricate/main.nf
+++ b/modules/hamronization/abricate/main.nf
@@ -8,7 +8,7 @@ process HAMRONIZATION_ABRICATE {
         'quay.io/biocontainers/hamronization:1.1.4--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path(report)
+    tuple val(meta), path(reports)
     val(format)
     val(software_version)
     val(reference_db_version)
@@ -23,16 +23,16 @@ process HAMRONIZATION_ABRICATE {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.sample_id}"
+    def prefix = task.ext.prefix ?: "${report.getBaseName()}"
     """
     hamronize \\
         abricate \\
-        ${report} \\
+        ${reports} \\
         $args \\
         --format ${format} \\
         --analysis_software_version ${software_version} \\
         --reference_database_version ${reference_db_version} \\
-        > ${prefix}.${format}
+        --output ${prefix}.${format}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/nextflow.config b/nextflow.config
index 7003f97..0a9f63f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -84,7 +84,7 @@ params {
 
 manifest {
     name = "bio-raum/gabi"
-    version = "0.9.1"
+    version = "0.9.2"
     description = "GABI Pipeline for assembly and profiling of bacterial isolates"
     author = "Marc Hoeppner"
     homePage = "https://github.com/bio-raum/gabi"
diff --git a/subworkflows/amr_profiling/main.nf b/subworkflows/amr_profiling/main.nf
index 8130322..ee857b5 100644
--- a/subworkflows/amr_profiling/main.nf
+++ b/subworkflows/amr_profiling/main.nf
@@ -77,7 +77,7 @@ workflow AMR_PROFILING {
 
     // Join basic Abricate results
     HAMRONIZATION_ABRICATE(
-        ABRICATE_RUN.out.report.mix(ABRICATE_RUN_ECOLI_VIRULENCE.out.report),
+        ABRICATE_RUN.out.report.mix(ABRICATE_RUN_ECOLI_VIRULENCE.out.report).groupTuple(),
         'json',
         '1.0.1',
         '2021-Mar-27'