add redirect for different pipeline links, switch to file based build format

astro.config.mjs

@@ -47,6 +47,7 @@ export default defineConfig({
  ],
  build: {
  inlineStylesheets: 'auto',
+ format: 'file',
  },
  vite: {
  plugins: [

public/_redirects

@@ -1,5 +1,6 @@
 /logo/* https://oldsite.nf-co.re/logo/:splat
 /tools/docs/* https://oldsite.nf-co.re/tools/docs//:splat
+/toosl/docs/2.9/* https://oldsite.nf-co.re/tools/docs/latest/:splat
 /community /contributors
 /pipeline_schema_builder/* https://oldsite.nf-co.re/pipeline_schema_builder/:splat
 /launch/* https://oldsite.nf-co.re/launch/:splat

public/components.json

@@ -26209,8 +26209,8 @@
  ]
  },
  "subworkflows": [
- "fastq_fastqc_umitools_fastp",
  "fastq_fastqc_umitools_trimgalore",
+ "fastq_fastqc_umitools_fastp",
  "fastq_trim_fastp_fastqc"
  ],
  "pipelines": [
@@ -59194,16 +59194,9 @@
  }
  },
  {
- "reads1": {
- "type": "file",
- "description": "fastq file paired end read 1",
- "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
- }
- },
- {
- "reads2": {
+ "reads": {
  "type": "file",
- "description": "fastq file paired end read 2",
+ "description": "List of input FastQ files of size 2; i.e., paired-end data.\n",
  "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
  }
  }
@@ -59225,7 +59218,21 @@
  {
  "merged_reads": {
  "type": "file",
- "description": "fastq file paired end read 2",
+ "description": "fastq file merged reads",
+ "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
+ }
+ },
+ {
+ "unstitched_read1": {
+ "type": "file",
+ "description": "fastq file unstitched read 1",
+ "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
+ }
+ },
+ {
+ "unstitched_read2": {
+ "type": "file",
+ "description": "fastq file unstitched read 2",
  "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
  }
  }
@@ -87253,8 +87260,10 @@
  "description": "The Java port of the VarDict variant caller",
  "keywords": [
  "variant calling",
- "VarDict",
- "AstraZeneca"
+ "vcf",
+ "bam",
+ "snv",
+ "sv"
  ],
  "tools": [
  {
@@ -87276,16 +87285,16 @@
  }
  },
  {
- "bam": {
+ "bams": {
  "type": "file",
- "description": "BAM/SAM file",
- "pattern": "*.{bam,sam}"
+ "description": "One or two BAM files. Supply two BAM files to run Vardict in paired mode.",
+ "pattern": "*.bam"
  }
  },
  {
- "bai": {
+ "bais": {
  "type": "file",
- "description": "Index of the BAM file",
+ "description": "Index/indices of the BAM file(s)",
  "pattern": "*.bai"
  }
  },
@@ -87296,13 +87305,25 @@
  "pattern": "*.bed"
  }
  },
+ {
+ "meta2": {
+ "type": "map",
+ "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n"
+ }
+ },
  {
  "fasta": {
  "type": "file",
  "description": "FASTA of the reference genome",
  "pattern": "*.{fa,fasta}"
  }
  },
+ {
+ "meta3": {
+ "type": "map",
+ "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n"
+ }
+ },
  {
  "fasta_fai": {
  "type": "file",