style: add publication metadata to all samtools modules

modules/nf-core/samtools/addreplacerg/meta.yml

@@ -13,6 +13,11 @@ tools:
       documentation: "https://www.htslib.org/doc/samtools-addreplacerg.html"
       tool_dev_url: "https://github.com/samtools/samtools"
       doi: "10.1093/bioinformatics/btp352"
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/ampliconclip/meta.yml

@@ -14,6 +14,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence:
         - "MIT"
       identifier: biotools:samtools

modules/nf-core/samtools/bam2fq/meta.yml

@@ -10,6 +10,12 @@ tools:
   - samtools:
       description: Tools for dealing with SAM, BAM and CRAM files
       documentation: http://www.htslib.org/doc/1.1/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence:
         - "MIT"
       identifier: biotools:samtools

modules/nf-core/samtools/bedcov/meta.yml

@@ -16,6 +16,11 @@ tools:
       documentation: "http://www.htslib.org/doc/samtools-bedcov.html"
       tool_dev_url: "https://github.com/samtools/samtools"
       doi: "10.1093/bioinformatics/btp352"
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence:
         - "MIT"
       identifier: biotools:samtools

modules/nf-core/samtools/bgzip/meta.yml

@@ -18,6 +18,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence:
         - "MIT"
       identifier: biotools:samtools

modules/nf-core/samtools/calmd/meta.yml

@@ -14,6 +14,11 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       tool_dev_url: "https://github.com/samtools/samtools"
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/cat/meta.yml

@@ -15,6 +15,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/collate/meta.yml

@@ -12,6 +12,11 @@ tools:
       documentation: "https://www.htslib.org/doc/samtools-collate.html"
       tool_dev_url: "https://github.com/samtools/samtools"
       doi: "10.1093/bioinformatics/btp352"
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/collatefastq/meta.yml

@@ -13,6 +13,11 @@ tools:
       documentation: "https://www.htslib.org/doc/samtools.html"
       tool_dev_url: "https://github.com/samtools/samtools"
       doi: "10.1093/bioinformatics/btp352"
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 

modules/nf-core/samtools/consensus/meta.yml

@@ -17,6 +17,11 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       tool_dev_url: "https://github.com/samtools/samtools"
       doi: "10.1093/bioinformatics/btp352"
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 

modules/nf-core/samtools/convert/meta.yml

@@ -14,6 +14,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/coverage/meta.yml

@@ -13,6 +13,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/cramsize/meta.yml

@@ -13,6 +13,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/depth/meta.yml

@@ -13,6 +13,11 @@ tools:
       documentation: http://www.htslib.org/doc/samtools-depth.html
       tool_dev_url: https://github.com/samtools/samtools
       doi: "10.1093/bioinformatics/btp352"
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence:
         - "MIT"
       identifier: biotools:samtools

modules/nf-core/samtools/dict/meta.yml

@@ -13,6 +13,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/faidx/meta.yml

@@ -15,6 +15,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence:
         - "MIT"
       identifier: biotools:samtools

modules/nf-core/samtools/fasta/meta.yml

@@ -12,6 +12,11 @@ tools:
       documentation: "https://www.htslib.org/doc/samtools-fasta.html"
       tool_dev_url: "https://github.com/samtools/samtools"
       doi: "10.1093/bioinformatics/btp352"
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/fastq/meta.yml

@@ -14,6 +14,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence:
         - "MIT"
       identifier: biotools:samtools

modules/nf-core/samtools/fixmate/meta.yml

@@ -21,6 +21,11 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       tool_dev_url: https://github.com/samtools/samtools
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/flagstat/meta.yml

@@ -17,6 +17,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence:
         - "MIT"
       identifier: biotools:samtools

modules/nf-core/samtools/getrg/meta.yml

@@ -16,6 +16,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/idxstats/meta.yml

@@ -17,6 +17,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence:
         - "MIT"
       identifier: biotools:samtools

modules/nf-core/samtools/import/meta.yml

@@ -16,6 +16,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/index/meta.yml

@@ -14,6 +14,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence:
         - "MIT"
       identifier: biotools:samtools

modules/nf-core/samtools/markdup/meta.yml

@@ -12,6 +12,11 @@ tools:
       documentation: "https://www.htslib.org/doc/samtools-markdup.html"
       tool_dev_url: "https://github.com/samtools/samtools"
       doi: "10.1093/bioinformatics/btp352"
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/merge/meta.yml

@@ -14,6 +14,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/mpileup/meta.yml

@@ -15,6 +15,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 input:

modules/nf-core/samtools/quickcheck/meta.yml

@@ -14,6 +14,11 @@ tools:
       documentation: "https://www.htslib.org/doc/samtools-quickcheck.html"
       tool_dev_url: "https://github.com/samtools/"
       doi: "10.1093/bioinformatics/btp352"
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools
 

modules/nf-core/samtools/reheader/meta.yml

@@ -16,6 +16,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence:
         - "MIT"
       identifier: biotools:samtools

modules/nf-core/samtools/samples/meta.yml

@@ -16,6 +16,11 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
+      publication:
+        author: "Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup"
+        year: 2009
+        title: "The Sequence Alignment/Map format and SAMtools"
+        source: "Bioinformatics"
       licence: ["MIT"]
       identifier: biotools:samtools