🔀 Merge pull request #13 from bunop/issue-8

➕ add est-sfs custom module dependency
bunop · Feb 26, 2024 · f4c267a · f4c267a
2 parents 638efb1 + 1813128
commit f4c267a
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Showing 8 changed files with 58 additions and 22 deletions.
diff --git a/tskit-pipeline/bin/est-sfs b/tskit-pipeline/bin/est-sfs
diff --git a/tskit-pipeline/conf/modules.config b/tskit-pipeline/conf/modules.config
@@ -89,6 +89,14 @@ process {
         ]
     }
 
+    withName: "GENERATE_SEED" {
+        publishDir = [
+            path: { "${params.outdir}/estsfs" },
+            mode: params.publish_dir_mode,
+            pattern: 'seedfile.txt'
+        ]
+    }
+
     withName: "TSINFER" {
         ext.args = { "--mutation_rate ${params.tsdate_mutation_rate} --ne ${params.tsdate_ne}" }
     }

diff --git a/tskit-pipeline/modules.json b/tskit-pipeline/modules.json
@@ -2,6 +2,17 @@
   "name": "tskit-pipeline",
   "homePage": "https://github.com/bunop/TSKITetude",
   "repos": {
+    "https://github.com/cnr-ibba/nf-modules.git": {
+      "modules": {
+        "cnr-ibba": {
+          "estsfs": {
+            "branch": "master",
+            "git_sha": "e9a3d75c0a0eb9743eeb791802f9a6876c155122",
+            "installed_by": ["modules"]
+          }
+        }
+      }
+    },
     "https://github.com/nf-core/modules.git": {
       "modules": {
         "nf-core": {
@@ -35,11 +46,6 @@
             "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
             "installed_by": ["modules"]
           },
-          "estsfs": {
-            "branch": "master",
-            "git_sha": "9678944d908e5aedab318c94a79d6ecbfa854fbc",
-            "installed_by": ["modules"]
-          },
           "plink/recode": {
             "branch": "master",
             "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",

diff --git a/...t-pipeline/modules/nf-core/estsfs/main.nf → ...-pipeline/modules/cnr-ibba/estsfs/main.nf b/...t-pipeline/modules/nf-core/estsfs/main.nf → ...-pipeline/modules/cnr-ibba/estsfs/main.nf
@@ -4,14 +4,15 @@ process ESTSFS {
     label 'process_long'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    container "docker.io/bunop/est-sfs:2.0.5"
 
     input:
-    tuple val(meta), path(e_config), path(data)
+    tuple val(meta), path(e_config), path(data), path(seed)
 
     output:
-    tuple val(meta), path("${prefix}_sfs.txt")   ,  emit: sfs_out
-    tuple val(meta), path("${prefix}_pvalues.txt"), emit: pvalues_out
-    tuple val(meta), path("${prefix}.seed"),        emit: seed
+    tuple val(meta), path("${prefix}_sfs.txt")      , emit: sfs_out
+    tuple val(meta), path("${prefix}_pvalues.txt")  , emit: pvalues_out
+    tuple val(meta), path("${prefix}.seed")         , emit: seed
     path "versions.yml", emit: versions
 
     when:
@@ -22,6 +23,7 @@ process ESTSFS {
     def VERSION = '2.05' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     prefix = task.ext.prefix ?: "${meta.id}"
     """
+    cp ${seed} ${prefix}.seed
     est-sfs ${e_config} ${data} ${prefix}.seed ${prefix}_sfs.txt ${prefix}_pvalues.txt
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/...-pipeline/modules/nf-core/estsfs/meta.yml → ...pipeline/modules/cnr-ibba/estsfs/meta.yml b/...-pipeline/modules/nf-core/estsfs/meta.yml → ...pipeline/modules/cnr-ibba/estsfs/meta.yml
diff --git a/tskit-pipeline/modules/local/tsinfer.nf b/tskit-pipeline/modules/local/tsinfer.nf
@@ -9,8 +9,7 @@ process TSINFER {
         "--volume ${HOME}/.cache/tsdate/:/.cache/tsdate/" }"""
 
     input:
-    tuple val(meta), path(vcf)
-    tuple val(meta2), path(ancestral)
+    tuple val(meta), path(vcf), path(ancestral)
     path(sample_file)
 
     output:

diff --git a/tskit-pipeline/nextflow.config b/tskit-pipeline/nextflow.config
@@ -96,21 +96,14 @@ profiles {
         cleanup                = false
         nextflow.enable.configProcessNamesValidation = true
     }
-    conda {
-        conda.enabled          = true
-        docker.enabled         = false
-        singularity.enabled    = false
-    }
     docker {
         docker.enabled         = true
-        conda.enabled          = false
         singularity.enabled    = false
         docker.runOptions      = '-u $(id -u):$(id -g)'
     }
     singularity {
         singularity.enabled    = true
         singularity.autoMounts = true
-        conda.enabled          = false
         docker.enabled         = false
     }
     test      { includeConfig 'conf/test.config'      }

diff --git a/tskit-pipeline/workflows/tskit.nf b/tskit-pipeline/workflows/tskit.nf
@@ -74,7 +74,7 @@ include {
     TABIX_TABIX as ANCIENT_SPLIT_TABIX      } from '../modules/nf-core/tabix/tabix/main'
 include { BCFTOOLS_MERGE                    } from '../modules/nf-core/bcftools/merge/main'
 include { ESTSFS_INPUT                      } from '../modules/local/estsfs_input'
-include { ESTSFS                            } from '../modules/nf-core/estsfs/main'
+include { ESTSFS                            } from '../modules/cnr-ibba/estsfs/main'
 include { ESTSFS_OUTPUT                     } from '../modules/local/estsfs_output'
 include { TSINFER                           } from '../modules/local/tsinfer'
 include { CUSTOM_DUMPSOFTWAREVERSIONS       } from '../modules/nf-core/custom/dumpsoftwareversions/main'
@@ -89,6 +89,16 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS       } from '../modules/nf-core/custom/du
 def multiqc_report = []
 
 
+process GENERATE_SEED {
+    output:
+    path 'seedfile.txt'
+
+    '''
+    echo $RANDOM > seedfile.txt
+    '''
+}
+
+
 workflow TSKIT {
     ch_versions = Channel.empty()
 
@@ -249,17 +259,35 @@ workflow TSKIT {
         outgroup_files_ch.collect()
     )
 
+    // determine a seedfile
+    seedfile = GENERATE_SEED()
+
+    // call custom est-sfs
     ESTSFS(
-        ESTSFS_INPUT.out.config.join(ESTSFS_INPUT.out.input)
+        ESTSFS_INPUT.out.config
+            .join(ESTSFS_INPUT.out.input)
+            .combine(seedfile)
     )
     ch_versions = ch_versions.mix(ESTSFS.out.versions)
 
     ESTSFS_OUTPUT(ESTSFS_INPUT.out.mapping.join(ESTSFS.out.pvalues_out))
 
+    tsinfer_in_ch = BCFTOOLS_REHEADER.out.vcf
+        .map{ meta, vcf -> [meta.chrom, meta, vcf] }
+        .join(
+            ESTSFS_OUTPUT.out.ancestral
+                .map{ meta, ancestral ->
+                        chrom = ancestral.name.tokenize(".")[-3]
+                        [chrom, ancestral]
+                },
+            by: [0],
+            failOnMismatch: true
+        ).map{ chrom, meta, vcf, ancestral -> [[id: meta.id], vcf, ancestral]}
+        // .view()
+
     // now create a tstree file
     TSINFER(
-        BCFTOOLS_REHEADER.out.vcf,
-        ESTSFS_OUTPUT.out.ancestral,
+        tsinfer_in_ch,
         samples_ch.first()
     )