From 344480193ea29c860c08e2be2ba8993d137f19a0 Mon Sep 17 00:00:00 2001
From: Paolo Cozzi <bunop@libero.it>
Date: Mon, 26 Feb 2024 17:46:14 +0100
Subject: [PATCH 1/6] :fire: remove est-sfs bin

---
 tskit-pipeline/bin/est-sfs | Bin 54792 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100755 tskit-pipeline/bin/est-sfs

diff --git a/tskit-pipeline/bin/est-sfs b/tskit-pipeline/bin/est-sfs
deleted file mode 100755
index 1d974b520167553f7e28756be2bd909053588b39..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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From e9c2ad379dca10bb30ee34daa7ae361a25e510da Mon Sep 17 00:00:00 2001
From: Paolo Cozzi <bunop@libero.it>
Date: Mon, 26 Feb 2024 18:01:41 +0100
Subject: [PATCH 2/6] :heavy_plus_sign: add custom estsfs module dependency

---
 tskit-pipeline/modules.json                   | 11 ++++
 .../modules/cnr-ibba/estsfs/main.nf           | 48 +++++++++++++++++
 .../modules/cnr-ibba/estsfs/meta.yml          | 53 +++++++++++++++++++
 3 files changed, 112 insertions(+)
 create mode 100644 tskit-pipeline/modules/cnr-ibba/estsfs/main.nf
 create mode 100644 tskit-pipeline/modules/cnr-ibba/estsfs/meta.yml

diff --git a/tskit-pipeline/modules.json b/tskit-pipeline/modules.json
index 7fe6362..713c2d6 100644
--- 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": "issue-33",
+            "git_sha": "e9a3d75c0a0eb9743eeb791802f9a6876c155122",
+            "installed_by": ["modules"]
+          }
+        }
+      }
+    },
     "https://github.com/nf-core/modules.git": {
       "modules": {
         "nf-core": {
diff --git a/tskit-pipeline/modules/cnr-ibba/estsfs/main.nf b/tskit-pipeline/modules/cnr-ibba/estsfs/main.nf
new file mode 100644
index 0000000..3028430
--- /dev/null
+++ b/tskit-pipeline/modules/cnr-ibba/estsfs/main.nf
@@ -0,0 +1,48 @@
+process ESTSFS {
+    tag "$meta.id"
+    label 'process_single'
+    label 'process_long'
+
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    container "docker.io/bunop/est-sfs:2.0.5"
+
+    input:
+    tuple val(meta), path(e_config), path(data), path(seed)
+
+    output:
+    tuple val(meta), path("${prefix}_sfs.txt")      , emit: sfs_out
+    tuple val(meta), path("${prefix}_pvalues.txt")  , emit: pvalues_out
+    tuple val(meta), path("${prefix}.seed")         , emit: seed
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    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 ${prefix}_pvalues.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        est-sfs: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_sfs.txt
+    touch ${prefix}_pvalues.txt
+    touch ${prefix}.seed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        est-sfs: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/tskit-pipeline/modules/cnr-ibba/estsfs/meta.yml b/tskit-pipeline/modules/cnr-ibba/estsfs/meta.yml
new file mode 100644
index 0000000..cae1988
--- /dev/null
+++ b/tskit-pipeline/modules/cnr-ibba/estsfs/meta.yml
@@ -0,0 +1,53 @@
+---
+name: "estsfs"
+description: estimation of the unfolded site frequency spectrum
+keywords:
+  - site frequency spectrum
+  - ancestral alleles
+  - derived alleles
+tools:
+  - "estsfs":
+      description: "est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation of a method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities by maximum likelihood (ML)."
+      homepage: "https://sourceforge.net/projects/est-usfs/"
+      documentation: "https://sourceforge.net/projects/est-usfs/"
+      tool_dev_url: "https://sourceforge.net/projects/est-usfs/files/est-sfs-release-2.04.tar.gz"
+      doi: "10.1534/genetics.118.301120"
+      licence: "['Free for Academic Use']"
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test']`
+  - e_config:
+      type: file
+      description: config file for est-sfs
+      pattern: "*.txt"
+  - data:
+      type: file
+      description: input data file for est-sfs
+      pattern: "*.txt"
+  - seed:
+      type: file
+      description: text file containing random number seed
+      pattern: "*.txt"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test']`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - sfs_out:
+      type: file
+      description: output file consists of the comma-separated estimated uSFS vector
+      pattern: "*.txt"
+  - pvalues_out:
+      type: file
+      description: this file contains the estimated ancestral state probabilities for each site
+      pattern: "*.txt"
+authors:
+  - "@BioInf2305"

From 1ab1bfdb48064c41e4173a2f96f8a72c210215ef Mon Sep 17 00:00:00 2001
From: Paolo Cozzi <bunop@libero.it>
Date: Mon, 26 Feb 2024 18:17:05 +0100
Subject: [PATCH 3/6] :sparkles: generate seed and call custom est-sfs

---
 tskit-pipeline/conf/modules.config |  8 ++++++++
 tskit-pipeline/modules.json        |  2 +-
 tskit-pipeline/workflows/tskit.nf  | 20 ++++++++++++++++++--
 3 files changed, 27 insertions(+), 3 deletions(-)

diff --git a/tskit-pipeline/conf/modules.config b/tskit-pipeline/conf/modules.config
index dab1477..fc8a8bc 100644
--- 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
index 713c2d6..9ef0840 100644
--- a/tskit-pipeline/modules.json
+++ b/tskit-pipeline/modules.json
@@ -6,7 +6,7 @@
       "modules": {
         "cnr-ibba": {
           "estsfs": {
-            "branch": "issue-33",
+            "branch": "master",
             "git_sha": "e9a3d75c0a0eb9743eeb791802f9a6876c155122",
             "installed_by": ["modules"]
           }
diff --git a/tskit-pipeline/workflows/tskit.nf b/tskit-pipeline/workflows/tskit.nf
index bd10c70..374abbf 100644
--- 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()
 
@@ -249,8 +259,14 @@ 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)
 

From e6a4060a50e11e6e07048e7b17cad7f583f57938 Mon Sep 17 00:00:00 2001
From: Paolo Cozzi <bunop@libero.it>
Date: Mon, 26 Feb 2024 18:19:44 +0100
Subject: [PATCH 4/6] :heavy_minus_sign: remove nf-core est-sfs dependency

---
 tskit-pipeline/modules.json                   |  5 --
 tskit-pipeline/modules/nf-core/estsfs/main.nf | 46 ----------------
 .../modules/nf-core/estsfs/meta.yml           | 53 -------------------
 3 files changed, 104 deletions(-)
 delete mode 100644 tskit-pipeline/modules/nf-core/estsfs/main.nf
 delete mode 100644 tskit-pipeline/modules/nf-core/estsfs/meta.yml

diff --git a/tskit-pipeline/modules.json b/tskit-pipeline/modules.json
index 9ef0840..fa6789f 100644
--- a/tskit-pipeline/modules.json
+++ b/tskit-pipeline/modules.json
@@ -46,11 +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/tskit-pipeline/modules/nf-core/estsfs/main.nf b/tskit-pipeline/modules/nf-core/estsfs/main.nf
deleted file mode 100644
index abeeb6f..0000000
--- a/tskit-pipeline/modules/nf-core/estsfs/main.nf
+++ /dev/null
@@ -1,46 +0,0 @@
-process ESTSFS {
-    tag "$meta.id"
-    label 'process_single'
-    label 'process_long'
-
-    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-
-    input:
-    tuple val(meta), path(e_config), path(data)
-
-    output:
-    tuple val(meta), path("${prefix}_sfs.txt")   ,  emit: sfs_out
-    tuple val(meta), path("${prefix}_pvalues.txt"), emit: pvalues_out
-    tuple val(meta), path("${prefix}.seed"),        emit: seed
-    path "versions.yml", emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    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}"
-    """
-    est-sfs ${e_config} ${data} ${prefix}.seed ${prefix}_sfs.txt ${prefix}_pvalues.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        est-sfs: $VERSION
-    END_VERSIONS
-    """
-
-    stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix}_sfs.txt
-    touch ${prefix}_pvalues.txt
-    touch ${prefix}.seed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        est-sfs: $VERSION
-    END_VERSIONS
-    """
-}
diff --git a/tskit-pipeline/modules/nf-core/estsfs/meta.yml b/tskit-pipeline/modules/nf-core/estsfs/meta.yml
deleted file mode 100644
index cae1988..0000000
--- a/tskit-pipeline/modules/nf-core/estsfs/meta.yml
+++ /dev/null
@@ -1,53 +0,0 @@
----
-name: "estsfs"
-description: estimation of the unfolded site frequency spectrum
-keywords:
-  - site frequency spectrum
-  - ancestral alleles
-  - derived alleles
-tools:
-  - "estsfs":
-      description: "est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation of a method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities by maximum likelihood (ML)."
-      homepage: "https://sourceforge.net/projects/est-usfs/"
-      documentation: "https://sourceforge.net/projects/est-usfs/"
-      tool_dev_url: "https://sourceforge.net/projects/est-usfs/files/est-sfs-release-2.04.tar.gz"
-      doi: "10.1534/genetics.118.301120"
-      licence: "['Free for Academic Use']"
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'test']`
-  - e_config:
-      type: file
-      description: config file for est-sfs
-      pattern: "*.txt"
-  - data:
-      type: file
-      description: input data file for est-sfs
-      pattern: "*.txt"
-  - seed:
-      type: file
-      description: text file containing random number seed
-      pattern: "*.txt"
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'test']`
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - sfs_out:
-      type: file
-      description: output file consists of the comma-separated estimated uSFS vector
-      pattern: "*.txt"
-  - pvalues_out:
-      type: file
-      description: this file contains the estimated ancestral state probabilities for each site
-      pattern: "*.txt"
-authors:
-  - "@BioInf2305"

From 9cf54b84e847b3a1c1383d8c3ec2040c06512d03 Mon Sep 17 00:00:00 2001
From: Paolo Cozzi <bunop@libero.it>
Date: Mon, 26 Feb 2024 19:20:07 +0100
Subject: [PATCH 5/6] :bug: fix issue with TSINFER input channels

using proper files pair
---
 tskit-pipeline/modules/local/tsinfer.nf |  3 +--
 tskit-pipeline/workflows/tskit.nf       | 16 ++++++++++++++--
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/tskit-pipeline/modules/local/tsinfer.nf b/tskit-pipeline/modules/local/tsinfer.nf
index 2ba9ba5..799fa5d 100644
--- 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/workflows/tskit.nf b/tskit-pipeline/workflows/tskit.nf
index 374abbf..7cf702e 100644
--- a/tskit-pipeline/workflows/tskit.nf
+++ b/tskit-pipeline/workflows/tskit.nf
@@ -272,10 +272,22 @@ workflow TSKIT {
 
     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()
     )
 

From 181312859df0c01954733018cb9e06d1975049b7 Mon Sep 17 00:00:00 2001
From: Paolo Cozzi <bunop@libero.it>
Date: Mon, 26 Feb 2024 19:21:38 +0100
Subject: [PATCH 6/6] :fire: drop conda profile

---
 tskit-pipeline/nextflow.config | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/tskit-pipeline/nextflow.config b/tskit-pipeline/nextflow.config
index 02ede5b..06b7498 100644
--- 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'      }