diff --git a/modules/sratools/prefetch/main.nf b/modules/sratools/prefetch/main.nf index 2233d0aa..3408c3e9 100644 --- a/modules/sratools/prefetch/main.nf +++ b/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' : - 'quay.io/biocontainers/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--pl5321ha49a11a_3' }" input: tuple val(meta), val(id) output: - tuple val(meta), path("$id"), emit: sra + tuple val(meta), path(id), emit: sra path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when - script: - def args = task.ext.args ?: '' - def config = "/LIBS/GUID = \"${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 '${config}' > "\${NCBI_SETTINGS}" - fi + shell: + args = task.ext.args ?: '' + args2 = task.ext.args2 ?: '5 1 100' // + config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n" - prefetch \\ - $args \\ - --progress \\ - $id - - vdb-validate $id - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+') - END_VERSIONS - """ + template 'retry_with_backoff.sh' } diff --git a/modules/sratools/prefetch/templates/retry_with_backoff.sh b/modules/sratools/prefetch/templates/retry_with_backoff.sh new file mode 100755 index 00000000..fbcb6532 --- /dev/null +++ b/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