Merge pull request #1627 from nf-core/fix-prefetch

Use a template to add retrying to prefetch

modules/sratools/prefetch/main.nf

@@ -1,43 +1,26 @@
 process SRATOOLS_PREFETCH {
     tag "$id"
     label 'process_low'
-    label 'error_retry'
 
     conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' :
+        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
-        'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0' }"
+        'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
 
     input:
     tuple val(meta), val(id)
 
     output:
-    tuple val(meta), path("$id"), emit: sra
+    tuple val(meta), path(id), emit: sra
     path "versions.yml"         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
-    script:
+    shell:
-    def args = task.ext.args ?: ''
+    args = task.ext.args ?: ''
-    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
+    args2 = task.ext.args2 ?: '5 1 100'  // <num retries> <base delay in seconds> <max delay in seconds>
-    """
+    config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
-    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
-    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
-        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
-        printf '${config}' > "\${NCBI_SETTINGS}"
-    fi
 
-    prefetch \\
+    template 'retry_with_backoff.sh'
-        $args \\
-        --progress \\
-        $id
-
-    vdb-validate $id
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
-    END_VERSIONS
-    """
 }

modules/sratools/prefetch/templates/retry_with_backoff.sh

@@ -0,0 +1,59 @@
+#!/usr/bin/env bash
+
+set -u
+
+retry_with_backoff() {
+    local max_attempts=${1}
+    local delay=${2}
+    local max_time=${3}
+    local attempt=1
+    local output=
+    local status=
+
+    # Remove the first three arguments to this function in order to access
+    # the 'real' command with `${@}`.
+    shift 3
+
+    while [ ${attempt} -le ${max_attempts} ]; do
+        output=$("${@}")
+        status=${?}
+
+        if [ ${status} -eq 0 ]; then
+            break
+        fi
+
+        if [ ${attempt} -lt ${max_attempts} ]; then
+            echo "Failed attempt ${attempt} of ${max_attempts}. Retrying in ${delay} s." >&2
+            sleep ${delay}
+        elif [ ${attempt} -eq ${max_attempts} ]; then
+            echo "Failed after ${attempt} attempts." >&2
+            return ${status}
+        fi
+
+        attempt=$(( ${attempt} + 1 ))
+        delay=$(( ${delay} * 2 ))
+        if [ ${delay} -ge ${max_time} ]; then
+            delay=${max_time}
+        fi
+    done
+
+    echo "${output}"
+}
+
+eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
+if [[ ! -f "${NCBI_SETTINGS}" ]]; then
+    mkdir -p "$(dirname "${NCBI_SETTINGS}")"
+    printf '!{config}' > "${NCBI_SETTINGS}"
+fi
+
+retry_with_backoff !{args2} \
+    prefetch \
+    !{args} \
+    !{id}
+
+vdb-validate !{id}
+
+cat <<-END_VERSIONS > versions.yml
+"!{task.process}":
+    sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
+END_VERSIONS